SII-SWORD/CoKE huggingface dataset:
Pfam PF00493: MCM P-loop domain (domain)
Proteins shown to be required for the initiation of eukaryotic DNA replication share a highly conserved domain of about 210 amino-acid residues . The latter shows some similarities  with that of various other families of DNA-dependent ATPases. Eukaryotes seem to possess a family of eight proteins that contain this domain. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called 'minichromosome maintenance proteins' with gene symbols prefixed by MCM. These six proteins are:


 * MCM2, also known as cdc19 (in S.pombe).
 * MCM3, also known as DNA polymerase alpha holoenzyme-associated protein P1, RLF beta subunit or ROA.
 * MCM4, also known as CDC54, cdc21 (in S.pombe) or dpa (in Drosophila).
 * MCM5, also known as CDC46 or nda4 (in S.pombe).
 * MCM6, also known as mis5 (in S.pombe).
 * MCM7, also known as CDC47 or Prolifera (in A.thaliana).
 * MCM8, also known as as REC (in Drosophila).
 * MCM


These proteins are evolutionarily related and belong to the AAA+ superfamily. They contain the Mcm family domain, which includes motifs that are required for ATP hydrolysis (such as the Walker A and B, and R-finger motifs). Mcm2-7 forms a hexameric complex which is the replicative helicase involved in replication initiation and elongation, whereas Mcm8 and Mcm9 from and separate one, conserved among many eukaryotes except yeast and C. elegans. Mcm8/9 complex play a role during replication elongation or recombination, being involved in the repair of double-stranded DNA breaks and DNA interstrand cross-links by homologous recombination. Drosophila is the only organism that has MCM8 without MCM9, involved in meiotic recombination .
Wikipedia: The minichromosome maintenance protein complex (MCM) is a DNA helicase essential for genomic DNA replication. Eukaryotic MCM consists of six gene products, Mcm2–7, which form a heterohexamer. As a critical protein for cell division, MCM is also the target of various checkpoint pathways, such as the S-phase entry and S-phase arrest checkpoints. Both the loading and activation of MCM helicase are strictly regulated and are coupled to cell growth cycles. Deregulation of MCM function has been linked to genomic instability and a variety of carcinomas.
Pfam PF18965: Outer capsid protein VP3-like (family)
This entry represents a group of Reoviridae proteins, including outer capsid protein VP3 from Cryphonectria parasitica mycoreovirus 1.
Pfam PF19717: Family of unknown function (DUF6212) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000801) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the galactoglucan biosynthetic gene cluster from Sinorhizobium  meliloti. This family appears to be predominantly found in  proteobacteria.
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 PF23391: Domain of unknown function (DUF7100) (domain)
This is an alpha-helical domain found at the N-terminal of a group of uncharacterised proteins from fungi. The function of this domain is unknown. Members of this entry also have a beta-propeller at the C-terminal ([pfam:PF23388]).
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 PF23727: FAM234A/B beta-propeller (repeat)
This entry represents the beta-propeller domain found in FAM234A/B proteins from mammals, whose function is unknown.
Pfam PF16250: Domain of unknown function (DUF4907) (family)
A family of uncharacterized proteins around 110 residues in length and found in various Bacteroides species. The function of this family is unknown.
Pfam PF13543: SAM like domain present in kinase suppressor RAS 1 (domain)
This SAM-like domain is found in kinase suppressor of Ras proteins, which are location-regulated scaffolding proteins connecting MEK to RAF . This domain is part of the N-terminal regulatory region that mediates heterodimerization of BRAF with KSR1.
Pfam PF03275: UDP-galactopyranose mutase (family)
UDP-galactopyranose mutase (5.4.99.9) is involved in the conversion of UDP-GALP into UDP-GALF through a 2-keto intermediate, and contains FAD as a cofactor. The gene is known as glf, ceoA, and rfbD. It is known experimentally in Escherichia coli, Mycobacterium tuberculosis, and Klebsiella pneumoniae.
Pfam PF01788: PsbJ (family)
This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria.  In Synechocystis sp. PCC 6803 PsbJ regulates the number of  photosystem II centres in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain.
Pfam PF09465: Lamin-B receptor of TUDOR domain (domain)
The Lamin-B receptor, found on the TUDOR domain [pfam:PF00567], is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner Nuclear Envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with Importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the NE.
Pfam PF17838: PH domain (domain)
This pleckstrin homology (PH) domain is found in some Rho guanine nucleotide exchange factors, such as ARHGEF18 (p114RhoGEF)  and ARHGEF1 (p115-RhoGEF) .
Pfam PF02495: Triple gene block 3 (family)
Family members include TGBp3 proteins found in many plant viruses. Triple gene block 3 proteins (TGBp3) are involved in virus momvement. TGBp3 is an integral ER membrane protein with a single transmembrane domain, and a C-terminal region exposed to the cytosol. TGBp3 is able to target TGBp2 to the cortical ER tubules of the cell periphery through the sorting signal in the C-terminal region of TGBp3. Moreover, it plays a key role in virus cell-to-cell movement by enhancing the TGBp2- and TGBp3-dependent plasmodesmata (PD) localization of TGBp1; however, the enhancement is abolished when one of the two conserved Cys residues in the C-terminal region of TGBp3 is replaced with Ala.
Pfam PF08089: Huwentoxin-II family (family)
This family consists of the huwentoxin-II (HWTX-II)  family of toxins secreted by spiders. These toxins are found in venom that secreted from the bird spider  Selenocosmia huwena Wang. The HWTX-II adopts a novel  scaffold different from the ICK motif that is found in  other huwentoxins. HWTX-II consists of 37 amino acids  residues including six cysteines involved in three disulfide bridges.
Pfam PF17096: Altered inheritance of mitochondria protein 3 (family)
AIM3 is a family of fungal proteins that are described as altered inheritance of mitochondria protein 3 proteins.
Pfam PF07309: Flagellar protein FlaF (family)
This family consists of several bacterial FlaF flagellar proteins. FlaF and FlaG are trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis.
Pfam PF22308: Domain of unknown function (DUF6969) (domain)
This domain is found in uncharacterised proteins from Proteobacteria. It is predicted to adopt an alpha/beta globular structure. It has three highly conserved histidines that are predicted to cluster together in space and are likely involved in metal coordination.
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 PF05778: Apolipoprotein CIII (Apo-CIII) (family)
This family consists of several mammalian apolipoprotein CIII (Apo-CIII) sequences. Apolipoprotein C-III is a 79-residue glycoprotein. It is synthesised in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by in vitro experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma.
Wikipedia: Apolipoprotein C-III also known as apo-CIII, and apolipoprotein C3, is a protein that in humans is encoded by the APOC3 gene. Apo-CIII is secreted by the liver as well as the small intestine, and is found on triglyceride-rich lipoproteins such as chylomicrons, very low density lipoprotein (VLDL), and remnant cholesterol.
Pfam PF15586: Immunity protein 8 (family)
A predicted immunity protein with an alpha+beta fold and a conserved WEa (a: aromatic) motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox7 family.
Pfam PF07280: Per os infectivity factor AC110 (family)
This family consists of several Baculovirus proteins of around 55 residues in length. Family members include Autographa californica nuclear polyhedrosis virus (AcMNPV) Per os infectivity factor AC110, which is required for oral infectivity. It may play a role after occlusion-derived virions pass through the host's peritrophic membrane.
Pfam PF13198: Protein of unknown function (DUF4014) (family)
This is a bacterial and viral family of uncharacterised 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 PF10703: MoaF N-terminal domain (domain)
MoaF protein is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha. It is conserved in Proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis. This entry corresponds to the N-terminal domain.
Pfam PF07639: YTV (repeat)
These hypothetical proteins in Rhodopirellula baltica contain several repeats of a sequence whose core is the residues YTV.
Pfam PF03578: HGWP repeat (repeat)
This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown.
Pfam PF16409: Domain of unknown function (DUF5017) (family)
This family of proteins is functionally uncharacterised. This family is found in various Bacteroides and Prevotella species. Proteins in this family are around 350 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 PF07647: SAM domain (Sterile alpha motif) (domain)
The sterile alpha motif (SAM) domain is a protein interaction module present in a wide variety of proteins  involved in many biological processes. The SAM domain that spreads over around 70 residues and one of the most common protein modules found in eukaryotic genomes . SAM domains have been shown to form homo- and hetero-oligomers, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins , nevertheless with a low affinity constant . SAM domains also appear to possess the ability to bind RNA . Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologues. These results suggest that the SAM domain might have a primary role in RNA binding.

Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces . In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures .
Wikipedia: In molecular biology, the protein domain Sterile alpha motif is a putative protein interaction module present in a wide variety of proteins involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins, nevertheless with a low affinity constant.
Pfam PF03131: bZIP Maf transcription factor (coiled_coil)
Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerisation and DNA binding property. Thus, this family is probably related to [pfam:PF00170]. This family also includes the DNA_binding domain of Skn-1 ([swissprot:P34707]), this domain lacks the leucine zipper found in other bZip domains, and binds DNA is a monomer.
Wikipedia: bZIP Maf is a domain found in Maf transcription factor proteins. It contains a leucine zipper (bZIP) domain, which mediates the transcription factor's dimerization and DNA binding properties. The Maf extended homology region (EHR) is present at the N-terminus of the protein. This region exists only within the Maf family and allows the family to recognize longer DNA motifs than other leucine zippers. These motifs are termed the Maf recognition element (MARE) and is 13 or 14 base pairs long. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region of the DNA. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor.
Pfam PF19433: Neuron-derived Neurotrophic Factor C-terminal (domain)
This is the C-terminal domain of Neuron-derived Neurotrophic Factor (NDNF). NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth of hippocampal neurons. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization. This domain contains the second fibronectin type III domain (FnIII) present in NDNF and one of the two potential consensus sites for N-linked glycosylation.
Pfam PF24543: Usp-48 domain (domain)
This entry represents a domain found towards the C-terminal of Ubiquitin carboxyl-terminal hydrolase usp-48 from C. elegans and related sequences from nematodes. Usp-48 is required post-developmentally to restrict the plasticity of epidermal cells, probably by regulating gene expression.
Pfam PF07313: N-acetylmuramoyl-L-alanine amidase-like (family)
This family includes N-acetylmuramoyl-L-alanine amidase (AMA) from Bacteroides uniformis and similar bacterial proteins. AmiA hydrolyses GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. It shows an alpha/beta/alpha three-layered sandwich fold with a catalytic core that consists of a central five-stranded beta-sheet and four alpha-helices. It is structurally related to NlpC/P60 gamma- D-Glu-meso-diaminopimelic acid amidases.
Pfam PF08858: IDEAL domain (domain)
This short domain is found at the C-terminus of proteins in the UPF0302 family.  The domain is named after the sequence of the most conserved region in some members.     The function of this domain is unknown.
Pfam PF21872: SAM domain-like (domain)
This entry corresponds to the most N-terminal SAM domain of several that is found topoisomerase V protein.
Wikipedia: In molecular biology, the protein domain Sterile alpha motif is a putative protein interaction module present in a wide variety of proteins involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins, nevertheless with a low affinity constant.
Pfam PF18767: Activation induced deaminase (family)
The activation induced deaminase is a vertebrate-specific member of the classical AID/APOBEC cytosine deaminases that is involved in antibody diversification.
Pfam PF03310: Caulimovirus DNA-binding protein (domain)
The gene III product of cauliflower mosaic virus (CaMV) is known as virion-associated protein or P3, which is tightly associated with the virus particles and has a regulatory function in the virus infection cycle. P3 decorate the virions; its N-terminal domain forms an antiparallel alpha-helical coiled-coil network at the surface and the C-terminal domain interacts with the C-terminal half of the coat protein. It is a DNA binding protein in which the DNA binding activity is located on its C-terminal part.
Pfam PF20556: Family of unknown function (DUF6768) (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 PF05439: Jumping translocation breakpoint protein (JTB) (family)
This family contains several jumping translocation breakpoint proteins or JTBs. Jumping translocation (JT) is an unbalanced translocation that comprises amplified chromosomal segments jumping to various telomeres. JTB, located at 1q21, has been found to fuse with the telomeric repeats of acceptor telomeres in a case of JT. hJTB (human JTB) encodes a trans-membrane protein that is highly conserved among divergent eukaryotic species. JT results in a hJTB truncation, which potentially produces an hJTB product devoid of the trans-membrane domain. hJTB is located in a gene-rich region at 1q21, called EDC (Epidermal Differentiation Complex). JTB has also been implicated in prostatic carcinomas.
Wikipedia: The jumping translocation breakpoint protein (JTB), also known as prostate androgen-regulated protein (PAR), is a protein that in humans is encoded by the JTB gene. It is an orphan receptor with unknown function.
Pfam PF01912: eIF-6 family (family)
This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues.
Pfam PF00036: EF hand domain (domain)
The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins.  The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site.  The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF11867: Type I restriction enzyme HindI endonuclease subunit-like, C-terminal (domain)
This domain is found at the C-terminal of Type I restriction enzyme HindI endonuclease subunit (also known as R protein) from Haemophilus influenzae related sequences from bacteria and archaea. This domain is typically between 255 to 340 amino acids in length and its function is unknown. This domain is found associated with [pfam:PF04851], [pfam:PF04313].
Pfam PF07087: Protein of unknown function (DUF1353) (family)
This family consists of several hypothetical bacterial proteins of around 100 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 PF08992: Quinohemoprotein amine dehydrogenase, gamma subunit (domain)
Members of this family contain a cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone, which is required for catalysis of the oxidative deamination of a wide range of aliphatic and aromatic amines. The domain assumes a globular secondary structure, with two short alpha-helices having many turns and bends.
Pfam PF24257: Family of unknown function (DUF7458) (family)
This entry represents a small family of uncharacterised mycobacterial phage. Some members are annotated as DNA primase. The family includes gene 53 from phage Bxb1.
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 PF15773: Dynein axonemal-associated protein 1 (family)
Daap1 is a axonemal dynein regulator that interacts with outer dynein arm (ODA) subunits and is required for deployment of ODA to the axoneme.
Pfam PF18094: DNA polymerase beta N-terminal domain (domain)
This is the N-terminal domain of DNA polymerase beta present in Homo sapiens.  DNA polymerase beta is a repair enzyme that has a key role in the base excision repair of simple DNA lesions.