SII-SWORD/CoKE huggingface dataset:
Pfam PF00522: VPR/VPX protein (family)
Human immunodeficiency virus (HIV) is the human retrovirus associated with AIDS (acquired immune deficiency syndrome), and SIV its simian counterpart. Three main groups of primate lentivirus are known, designated Human immunodeficiency virus 1 (HIV-1), Human immunodeficiency virus 2 (HIV-2)/Simian immunodeficiency virus - mac (SIVMAC)/Simian immunodeficiency virus - sm (SIVSM) and Simian immunodeficiency virus - agm (SIVAGM). Simian immunodeficiency virus - mnd (SIVMND) has been suggested to represent a fourth distinct group . These groups are believed to have diverged from a common ancestor long before the spread of AIDS in humans. Genetic variation in HIV-1 and HIV-2 has been studied extensively, and the nucleotide sequences reported for several strains .

ORF analysis has revealed two open reading frames, yielding the so-called R- and X-ORF proteins, which show a high degree of sequence similarity.

Vpx plays a role in nuclear translocation of the viral pre-integration complex (PIC) and is thus required for the virus to infect non-dividing cells. Vpr also plays a role in nuclear translocation of the (PIC) and may target specific host proteins for degradation by the 26S proteasome. It acts by associating with the cellular CUL4A-DDB1 E3 ligase complex through direct interaction with host VPRPB/DCAF-1. This would result in cell cycle arrest or apoptosis in infected cells, creating a favourable environment for maximizing viral expression and production by rendering the HIV-1 LTR transcription more active.
Wikipedia: Vpr is a Human immunodeficiency virus gene and protein product. Vpr stands for "Viral Protein R". Vpr, a 96 amino acid 14-kDa protein, plays an important role in regulating nuclear import of the HIV-1 pre-integration complex, and is required for virus replication and enhanced gene expression from provirus in dividing or non-dividing cells such as T cells or macrophages. Vpr also induces G2 cell cycle arrest and apoptosis in proliferating cells, which can result in immune dysfunction.
Pfam PF19426: Mesoderm induction early response protein 1/3 C-terminal (domain)
This domain is found at the C-terminal of MIER1 and MIER3. MIER1 is a transcriptional repressor that regulates the expression of a number of genes including SP1 target genes, recruiting histone deacetylase 1 (HDAC1) through its ELM2 domain. It has two isoforms, alpha and beta, which differ in their C-terminal domains, both of them being able to interact with HDAC1. The gene encoding MIER3 has been identified as a candidate cancer susceptibility gene. MIER1 and 3 share two regions of high homology, one at the N-terminal and the second at the C-terminal, represented in this entry, which includes a short region located immediately downstream of the SANT extension that is 84% identical.
Pfam PF18818: Zincin-like metallopeptidase (family)
Zincin-like Metallopeptidase frequently found in polyvalent proteins  of phages and conjugative elements. The active site is comprised of  a HEXXH motif and a C-terminal glutamate.
Pfam PF23396: Family of unknown function (DUF7103) (family)
This is a family of unknown function. It is structurally similar to Frag1-like domain, composed of a six-alpha-helix bundle transmembrane region.
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 PF23652: TRAPP14 C-terminal (domain)
This entry includes Trafficking protein particle complex subunit 14 (TRAPP14), which is a specific subunit of the TRAPP (transport protein particle) II complex, a conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether. This entry represents the C-terminal domain which may adopt a Ig-like fold.
Pfam PF11951: Fungal specific transcription factor domain (family)
This family of are likely to be transcription factors. This protein is found in fungi. Proteins in this family are typically between 454 to 826 amino acids in length. This protein is found associated with [pfam:PF00172].
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 PF15976: CS1-pili formation C-terminal (family)
CooC_C is a highly conserved C-terminal domain on fimbrial outer membrane usher proteins like TcfC. The protein is required for CS1 pilus formation.
Pfam PF19545: Family of unknown function (DUF6069) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001769) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the family saquayamycin A biosynthetic gene cluster  from Streptomyces sp. and appears to be predominantly found in  Actinobacteria.
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 PF09509: Protein of unknown function (Hypoth_ymh) (family)
This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown.
Pfam PF05276: SH3 domain-binding protein 5 (SH3BP5) (family)
This family consists of several eukaryotic SH3 domain-binding protein 5 or c-Jun N-terminal kinase (JNK)-interacting proteins (SH3BP5 or Sab). Sab binds to and serves as a substrate for JNK in vitro, and has been found to interact with the Src homology 3 (SH3) domain of Bruton's tyrosine kinase (Btk).  Inspection of the sequence of Sab reveals the presence of two putative mitogen-activated protein kinase interaction motifs (KIMs) similar to that found in the JNK docking domain of the c-Jun transcription factor, and four potential serine-proline JNK phosphorylation sites in the C-terminal half of the molecule.
Pfam PF24331: Mycobacterial phage zinc binding domain (domain)
This entry represents a small zinc binding domain found in a small family of uncharacterised mycobacterium phage proteins.
Pfam PF20948: Influenza RNA polymerase PB2 second domain (domain)
Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. This entry represents the domain of the Flu PB protein that follows the N-terminal extended region.
Pfam PF16032: Domain of unknown function (DUF4788) (domain)
This presumed domain is functionally uncharacterised. This domain is found in insects, and is approximately 230 amino acids in length. There is a single completely conserved residue D that may be functionally important. It adopts a C2-like fold.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14849: YidC periplasmic domain (domain)
This is the periplasmic domain of YidC, a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins.
Pfam PF02603: HPr Serine kinase N terminus (family)
This family represents the N-terminal region of Hpr Serine/threonine kinase PtsK.  This kinase is the sensor in a multicomponent phospho-relay system in control of carbon catabolic repression in bacteria.  This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF17062: Outer spore wall 5 (family)
In fungi the outermost cape of the spore wall is made up of a polymer that contains cross-linked amino acid dityrosine, which is important for the stress resistance of the spore. The OSW family of proteins have been implicated in assembly of this protective dityrosine coat. OSW5 null mutant spores show an enhanced spore wall permeability and vulnerability to beta glucanase digestion. The proteins are predicted to be integral membrane proteins.
Pfam PF07109: Magnesium-protoporphyrin IX methyltransferase C-terminus (family)
This family represents the C-terminus (approximately 100 residues) of bacterial and eukaryotic Magnesium-protoporphyrin IX methyltransferase ([ec:2.1.1.11]). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX methylester using S-adenosyl-L-methionine as a cofactor.
Pfam PF07112: Protein of unknown function (DUF1368) (family)
This family consists of several proteins with seem to be specific to red algae plasmids. Members of this family are typically around 415 residues in length. The function of this family is unknown.
Pfam PF02898: Nitric oxide synthase, oxygenase domain (domain)
This entry represents the N-terminal of the nitric oxide synthases.
Nitric oxide synthase (1.14.13.39) (NOS) enzymes produce nitric oxide (NO) by catalysing a five-electron oxidation of a guanidino nitrogen of L-arginine (L-Arg). Oxidation of L-Arg to L-citrulline occurs via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine as an intermediate. 2 mol of O(2) and 1.5 mol of NADPH are consumed per mole of NO formed .

Arginine-derived NO synthesis has been identified in mammals, fish, birds, invertebrates, plants, and bacteria . Best studied are mammals, where three distinct genes encode NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . iNOS and nNOS are soluble and found predominantly in the cytosol, while eNOS is membrane associated. The enzymes exist as homodimers, each monomer consisting of two major domains: an N-terminal oxygenase domain, which belongs to the class of haem-thiolate proteins, and a C-terminal reductase domain, which is homologous to NADPH:P450 reductase (1.6.2.4). The interdomain linker between the oxygenase and reductase domains contains a calmodulin (CaM)-binding sequence. NOSs are the only enzymes known to simultaneously require five bound cofactors animal NOS isozymes are catalytically self-sufficient. The electron flow in the NO synthase reaction is: NADPH -->FAD -->FMN -->haem -->O(2).

eNOS localisation to endothelial membranes is mediated by cotranslational N-terminal myristoylation and post-translational palmitoylation . The subcellular localisation of nNOS in skeletal muscle is mediated by anchoring of nNOS to dystrophin. nNOS contains an additional N-terminal domain, the PDZ domain . Some bacteria, like Bacillus halodurans, Bacillus subtilis or Deinococcus radiodurans, contain homologues of NOS oxygenase domain.
Wikipedia: Nitric oxide synthases (NOSs) are a family of enzymes catalyzing the production of nitric oxide (NO) from L-arginine. NO is an important cellular signaling molecule. It helps modulate vascular tone, insulin secretion, airway tone, and peristalsis, and is involved in angiogenesis and neural development. It may function as a retrograde neurotransmitter. Nitric oxide is mediated in mammals by the calcium-calmodulin controlled isoenzymes eNOS and nNOS. The inducible isoform, iNOS, involved in immune response, binds calmodulin at physiologically relevant concentrations, and produces NO as an immune defense mechanism, as NO is a free radical with an unpaired electron. It is the proximate cause of septic shock and may function in autoimmune disease.
Pfam PF20155: Tape measure protein (family)
This entry represents phage tape measure proteins that are required to assemble the page tail. The protein serves as a base for tail tube protein polymerization and acts as a template for tail length determination. This family is likely related to [pfam:PF10145].
Pfam PF04369: Lactococcin-like family (family)
Family of bacteriocins from lactic acid bacteria.
Wikipedia: Bacteriocins are proteinaceous or peptidic toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). They are similar to yeast and paramecium killing factors, and are structurally, functionally, and ecologically diverse. Applications of bacteriocins are being tested to assess their application as narrow-spectrum antibiotics.
Pfam PF22969: NUP210 Ig-like domain 2 (domain)
This domain is found in the homologues of human Nuclear pore membrane glycoprotein 210 (NUP210). NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.
Pfam PF04808: Citrus tristeza virus (CTV) P23 protein (family)
This family consists of protein P23 from the citrus tristeza virus, which is a member of the Closteroviridae.      CTV viruses produce more positive than negative RNA strands, and P23 controls this asymmetrical RNA accumulation. Amino acids 42-180 are essential for function and are thought to contain RNA-binding and zinc finger domains.
Pfam PF07511: Protein of unknown function (DUF1525) (family)
This entry represents a group of proteins predominantly found in Gammaproteobacteria. Members belong to extended genomic regions that appear to be spread by conjugative transfer .
Pfam PF22508: Internalin J, Immunoglobulin-like domain (domain)
This entry represents a immunoglobulin-like domain present in the Internalin J (InlJ) protein from Listeria monocytogenes.
Pfam PF23208: ZNF598 C2H2 zinc finger domain (domain)
This C2H2 zinc finger domain is found in human E3 ubiquitin-protein ligase ZNF598 and related eukaryotic proteins. ZNF598 plays a key role in the ribosome quality control (RQC), a pathway that takes place when the ribosome has stalled during translation, leading to degradation of nascent peptide chains. ZNF598 is activated when ribosomes are stalled following translation of prematurely polyadenylated mRNAs. Independently of its role in RQC, this protein may also act as a negative regulator of interferon-stimulated gene expression.
Pfam PF19667: Family of unknown function (DUF6170) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 84 and 107 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 PF03880: DbpA RNA binding domain (domain)
This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins.  It is sufficient to confer specificity  for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data].
Pfam PF22488: Class 2 C-terminal docking domain (domain)
This short domain is found at the C-terminal end of the polyketide synthase module CurG from the cyanobacteria Moorena producens. It consists of two alpha-helices connected by a sharp bend.
Pfam PF06908: YspA SLOG family (family)
Family in the SLOG superfamily showing fusions to NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by the associating enzymes.
Pfam PF03583: Secretory lipase (family)
These lipases are expressed and secreted during the infection cycle of these pathogens.  In particular, C. albicans has  a large number of different lipases, possibly reflecting broad lipolytic activity, which may contribute to the persistence and virulence of C. albicans in human tissue.
Pfam PF22762: NrS-1 polymerase-like, tail domain (domain)
This entry represents the tail domain found in NrS-1 polymerase from Nitratiruptor phage NrS-1, the first known phage that can infect Epsilonproteobacteria, one of the predominant primary producers in the deep-sea hydrothermal vent ecosystems. NrS-1 polymerase is a multidomain enzyme and is a key component of the phage replisome. This domain, together with the head ([pfam:PF22761]) and helicase ([pfam:PF19263]) domains, is responsible for the DNA activity in this protein. It has a novel alpha/beta fold.The tail domain is important for the hexamer assembly and polymerization activity of NrS-1 polymerase.
Pfam PF22785: Polymorphic toxin system, DSP-PTPase phosphatase (domain)
This domain occupies the toxin tip position in a subset of polymorphic toxin domains. This domain is found at the extreme C-terminal of certain polymorphic toxin-related Tc-like toxins deployed by bacteria against eukaryotic host cells. This position is where the toxin module delivered into the target cells host resides.
Pfam PF13508: Acetyltransferase (GNAT) domain (domain)
This domain catalyses N-acetyltransferase reactions.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF01869: BadF/BadG/BcrA/BcrD ATPase family (family)
This family includes the BadF [swissprot:O07462] and BadG [swissprot:O07463] proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase [swissprot:P11568]. The protein [swissprot:O66634] contains two copies of this region suggesting that the family may structurally dimerise. This family appears to be related to [pfam:PF00370].
Pfam PF07147: Mitochondrial 28S ribosomal protein S30 (PDCD9) (family)
This family consists of several eukaryotic mitochondrial 28S ribosomal protein S30 (or programmed cell death protein 9 PDCD9) sequences. The exact function of this family is unknown although it is known to be a component of the mitochondrial ribosome and a component in cellular apoptotic signaling pathways.
Pfam PF25112: AtTam37 zinc finger region (domain)
This domain is found in the AtTam37 from Arabidopsis thaliana and related proteins. AtTam37 is an essential component of the chloroplast import motor. It serves as a  molecular chaperone within the AtYcf2-FtsHi complex. The domain represented by this entry contains four highly conserved pairs of cysteine residues which are involved in the coordination of two zinc ions.
Pfam PF14852: Fis1 N-terminal tetratricopeptide repeat (repeat)
The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the N-terminal tetratricopeptide repeat
Pfam PF12979: Domain of Unknown Function with PDB structure (DUF3863) (domain)
Domain based on 1-364 domain of PDB:3LM3 which is encoded by the BDI_3119 gene from Parabacteroides distasonis atcc 8503.
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 PF20622: Bacterial Ig domain (Big_16) (domain)
This bacterial Ig-like domain is found in the stalk regions of bacterial cell surface adhesins.
Pfam PF11851: Domain of unknown function (DUF3371) (family)
This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 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 PF05684: Protein of unknown function (DUF819) (family)
This family contains proteins of unknown function from archaeal, bacterial and plant species.
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.