SII-SWORD/CoKE huggingface dataset:
Pfam PF03538: Salmonella virulence plasmid 28.1kDa A protein (family)
This entry included insecticidal toxin complex proteins (TcaA, TccA, TcbA, TcdA) from Photorhabdus luminescens subsp. laumondii and Xenorhabdus nematophilus (Achromobacter nematophilus) , and virulence proteins from Salmonella typhimurium that are encoded on a 90kb plasmid.

P. luminescens and X. nematophilus are Gram-negative bacteria that form entomopathogenic symbioses with soil nematodes. The bacteria are found in the gut of entomopathogenic nematodes that invade and kill insects. When the nematode invades an insect host the bacteria are released into the insect haemocoel (the open circulatory system), both the bacteria and the nematode undergo multiple rounds of replication which kills the insect host. Mapping of the insecticidal toxin loci and studies on knockout mutants in P. luminescens showed that deletion of either tca or tcd loci dramatically reduced toxicity, while the double mutant tca/tcd abolished toxicity . However the biology of toxin action is unclear as is the species range of insects the toxins are active against.

S. typhimurium contains a 90kb plasmid that is associated with virulence. This plasmid encodes at least 6 genes needed by the bacterium for invading host macrophages during infection. These include the 70kDa mkaA protein , a recognised virulence factor, and more recently described, four spv genes under the control of a regulator .

Deletion studies on the virulence plasmid have shown that an open reading frame encoding a 28kDa protein was needed for successful invasion of the host. This protein, designated mkfA , VRP4  or VirA  by different groups, is utilised by the microbe upon entry into macrophages, although the exact mechanism is unclear.
Pfam PF09952: Transcriptional regulator, AbiEi antitoxin, Type IV TA system (family)
AbiEi_2 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is [pfam:PF13338].
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF20328: Family of unknown function (DUF6623) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 147 and 199 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 PF15677: Cell cycle exit and neuronal differentiation protein 1 (family)
This family of neuron-specific proteins may have a role in the differentiation of neuroblastoma cells and neuronal precursors. It is involved in development of the cerebellum.
Pfam PF23306: VPS8-like, N-terminal beta propeller repeats (repeat)
This entry represents the N-terminal region of human Vacuolar protein sorting-associated protein 8 homolog (VPS8) and similar eukaryotic proteins. VPS8 plays a role in vesicle-mediated protein trafficking of the endocytic membrane transport pathway. This region contains several repeats predicted to form part of a beta propeller.
Pfam PF21257: ASH2, PHD zinc finger (domain)
Set1/Ash2 histone methyltransferase complex subunit ASH2 from humans (ASH2L, named after 'Absent, small, homeotic disks-2-like') is a component of the Set1/Ash2 histone methyltransferase (HMT) complex and has an important role in regulating the methylation of histone H3 on lysine 4. It consists of an atypical PDH finger at the N-temrinal, represented in this entry, followed by a winged-helix ([pfam:PF21198]) and a C-terminal SPRY domain ([pfam:PF00622]). This domain does not have histone tail-binding activity.
Pfam PF00905: Penicillin binding protein transpeptidase domain (domain)
The active site serine (residue 337 in [swissprot:P14677]) is conserved in all members of this family.
Wikipedia: Penicillin-binding proteins (PBPs) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent of many bacteria; the name just reflects the way by which the protein was discovered. All β-lactam antibiotics bind to PBPs, which are essential for bacterial cell wall synthesis. PBPs are members of a subgroup of transpeptidase enzymes called DD-transpeptidases.
Pfam PF08746: RING-like domain (domain)
This is a zinc finger domain that is related to the C3HC4 RING finger domain ([pfam:PF00097]).
Wikipedia: In molecular biology, a RING (short for Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Conversely, proteins with RING finger domains are the largest type of ubiquitin ligases in the human genome.
Pfam PF01900: Rpp14/Pop5 family (family)
tRNA processing enzyme ribonuclease P (RNase P) is a ubiquitous ribozyme that catalyzes a Mg2-dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA). Archaeal and eukaryotic RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins. Human RNase P is composed of a singular protein Pop1 and three subcomplexes, the Rpp20-Rpp25 heterodimer, Pop5-Rpp14- (Rpp30)2-Rpp40 heteropentamer, and Rpp21-Rpp29-Rpp38 heterotrimer. This family includes Rnp2 (also known as Pop5) from archaea and Pop5/Rpp14 from eukaryotes.
Pfam PF03007: Wax ester synthase/diacylglycerol acyltransferase catalytic domain (domain)
This domain is found in wax ester synthases/diacylglycerol O-acyltransferases (WS/DAGs), largely found in bacteria, plants and animals. They catalyse the condensation of a fatty alcohol and a fatty acyl-Coenzyme A (acyl-CoA) and they can also catalyse the transesterification of acyl-CoAs with diacylglycerols. These are bifunctional enzymes (WS/DAGs) that share low overall sequence similarity but all WS/DGATs share a conserved HHXXXDG motif, which is also found in other acyltransferases. This entry represents the N-terminal catalytic domain of WS/DAGs which contains the conserved HHXXXDG motif. It consists of a mixed beta-sheet flanked by four alpha-helices and a small antiparallel beta-sheet.
Pfam PF18792: Ubiquitous surface protein adhesin repeat (repeat)
The UspA1 head domain is globally similar to other structures of TAA  head domains and comprises a trimeric left-handed parallel beta-roll, which is formed from 14 repeating 14-16 residue segments that form  a ladder of beta-strand coils. This Pfam entry represents a  single repeat unit of the beta-ladder.
Pfam PF03982: Diacylglycerol acyltransferase (family)
The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT), required for synthesis and storage of intracellular triglycerides. In yeast, it is involved in lipid particle synthesis from the endoplasmic reticulum (ER), promoting localised TAG production at discrete ER subdomains, and in ergosterol biosynthesis. This family also includes Acyl-CoA wax alcohol acyltransferase 1 and 2 (AWAT1/2) which catalyse  the formation of ester bonds between fatty alcohols and fatty acyl-CoAs to form wax monoesters. AWAT2 (also known as MFAT) also possesses acyl-CoA retinol acyltransferase (ARAT) activity that catalyses 11-cis-specific retinyl ester synthesis and shows higher catalytic efficiency toward 11-cis-retinol versus 9-cis-retinol, 13-cis-retinol, and all-trans-retinol substrates.
Pfam PF05832: Eukaryotic protein of unknown function (DUF846) (family)
This family consists of several of unknown function from a variety of eukaryotic organisms.
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 PF19732: Stage II sporulation protein E N-terminal (domain)
This is the N-terminal domain found in Stage II sporulation protein E which includes the 10 transmembrane domains and the regulatory domain, the latter located adjacent the PP2C phosphatase domain. The regulatory domain mediates the formation of dimers between SpoIIE molecules, required for phosphatase activation. An N-terminal 45-residue long alpha-helix makes intramolecular contacts with the switch helices (alpha1 and alpha2) of the phosphatase domain.
Pfam PF21151: COP9 signalosome complex subunit 1, C-terminal helix (domain)
This is the C-terminal helix from COP9 signalosome complex subunit 1, an essential component of the COP9 signalosome complex (CSN), which involved in various cellular and developmental processes.
Pfam PF05625: PAXNEB protein (domain)
PAXNEB or PAX6 neighbour is found in several eukaryotic organisms.  PAXNED is an RNA polymerase II Elongator protein subunit. It is part of the HAP subcomplex of Elongator, which is a six-subunit component of the RNA polymerase II holoenzyme. The HAP subcomplex is required for Elongator structural integrity and histone acetyltransferase activity. This protein family has a P-loop-like motif and adopts a RecA-ATPase-like fold, lacking the conserved sequence signature of ATPases.
Pfam PF24565: Nuclear elongation and deformation protein 1-like, middle domain (domain)
This domain is centrally located in Nuclear elongation and deformation protein 1 from Schizosaccharomyces pombe (Ned1) and similar fungal proteins. Ned1 may have a role in the maintenance of the nuclear envelope structure and in minichromosome stability. This domain is predicted to adopt an alpha-beta structure.
Pfam PF01250: Ribosomal protein S6 (domain)
The small subunits of bacterial and eukaryotic ribosomes have the same overall shapes (with structural elements described as head, body, platform, beak and shoulder). Ribosomal protein bS6 is one of the proteins from the small ribosomal subunit. . In Escherichia coli, bS6 is known to bind together with bS18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle bS6 ribosomal proteins.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF14549: DNA-binding transcriptional regulator Cro (domain)
Bacteriophage P22 Cro protein represses genes normally expressed in early phage development and is necessary for the late stage of lytic growth.  It does this by binding to the OL and OR operator-regions normally used by the repressor protein for lysogenic maintenance.
Pfam PF00550: Phosphopantetheine attachment site (domain)
A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of [swissprot:P19828] has the attachment serine replaced by an alanine.
Wikipedia: The acyl carrier protein (ACP) is a cofactor of both fatty acid and polyketide biosynthesis machinery. It is one of the most abundant proteins in cells of E. coli. In both cases, the growing chain is bound to the ACP via a thioester derived from the distal thiol of a 4'-phosphopantetheine moiety.
Pfam PF11955: Plant organelle RNA recognition domain (family)
This family, which was previously known as DUF860, has been shown to be a component of group II intron ribonucleoprotein particles in maize chloroplasts. The domain is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. All of the members are predicted to localise to mitochondria or chloroplasts. It seems likely that most PORR proteins function in organellar RNA metabolism.
Pfam PF18560: Lectin like domain (domain)
This is a lectin like domain found in Cwp84, a surface-located cysteine protease (a member of the C1A cysteine protease family, also known as papain proteases) responsible for the maturation of the SlpA precursor protein which has been implicated in the degradation of extracellular matrix proteins such as fibronectin, laminin and vitronectin. Structural comparison indicates that this domain is similar to carbohydrate-binding domains.
Pfam PF07948: Nairovirus GP38 (domain)
This entry represents the GP38 secreted glycoprotein from nairoviruses, including CCHFV and Dugbe virus. It is encoded in the glycoprotein precursor complex (GPC) from the M segment of nairovirus  genome. It has a novel fold composed of a 3-helix bundle and a beta-sandwich. Although its function is unknown, it is immunogenic in humans and, therefore, an interesting vaccine target.
Pfam PF09959: Uncharacterized protein conserved in archaea (DUF2193) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09309: FCP1, C-terminal (domain)
The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains.
Pfam PF11430: Programmed cell death activator EGL-1 (family)
Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended alpha-helical conformation.
Pfam PF03324: Herpesvirus DNA helicase/primase complex associated protein (family)
This family includes  HSV UL8, EHV-1 54, VZV 52 AND HCMV 102.
Pfam PF20569: Family of unknown function (DUF6778) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, predominantly in Rhodobacteria. Proteins in this family are typically between 203 and 225 amino acids in length. This family contains the conserved sequence motifs DIVW, RFH and GGxH.
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 PF15803: Zinc-finger of sodium channel modifier 1 (family)
zf-SCNM1 is a C2H2 type zinc-finger conserved in eukaryotes found at the N-terminus of SCNM1, sodium channel modifier protein 1. Phylogenetic analysis of these zinc finger sequences places SCNM1 within the U1C subfamily of RNA binding proteins that is commonly found in RNA-processing proteins, suggesting that SCNM1 is involved in splicing activities.
Pfam PF11650: P22 tail accessory factor (family)
This tail accessory factor of the P22 virus is also referred to as gene product 4 (Gp4). The proteins structure consists of 60% alpha helices. Gp4 is the first tail accessory factor to be added to newly DNA-filled capsids during P22-morphogenesis. In solution, the protein acts as a monomer and has low structural stability. The interaction of gp4 with the portal protein involves the binding of two non-equivalent sets of six gp4 proteins. Gp4 acts as a structural adaptor for gp10 and gp26, the other tail accessory factors.
Wikipedia: Salmonella virus P22 is a bacteriophage in the Podoviridae family that infects Salmonella typhimurium. Like many phages, it has been used in molecular biology to induce mutations in cultured bacteria and to introduce foreign genetic material. P22 has been used in generalized transduction and is an important tool for investigating Salmonella genetics.
Pfam PF06278: Condensin II complex subunit CAP-H2 or CNDH2, N-terminal (family)
CNDH2_N is the N-terminal domain of the H2 subunit of the condensing II complex, found in eukaryotes but not in fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits.  The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII is concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi.  CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2.  All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex).  The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII.
Pfam PF09779: Ima1 N-terminal domain (family)
This domain occurs at the N-terminus of the Schizosaccharomyces pombe inner nuclear membrane (INM) protein, Ima1. Ima1 interacts with other  inner nuclear membrane proteins.
Pfam PF21926: N-acyl amino acid synthase FeeM (domain)
This entry represents the catalytic core of the N-acyl amino acid synthase FeeM. This domain folds into a central antiparallel beta-sheet packed on both sides with alpha-helices and closely resembles the conserved core of GNAT superfamily.
Pfam PF22618: Anti-sigma-K factor RskA, N-terminal domain (domain)
This domain is found at the N-terminal end of the anti-sigma-K factor from Mycobacterium tuberculosis (RskA), which positively regulates expression of the antigenic proteins MPB70 and MPB83.
Pfam PF07548: Chlamydia polymorphic membrane protein middle domain (family)
This family contains several Chlamydia polymorphic membrane proteins.  Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract.  This domain is found between the beta-helical repeats ([pfam:PF02415]) and the C-terminal [pfam:PF03797]. This domain is excised subsequent to secretion.
Pfam PF09801: Integral membrane protein S linking to the trans Golgi network (family)
Members of this family are integral membrane proteins involved in protein trafficking between the late Golgi and endosome. They may also serve as a receptor for ADP-ribosylation factor-related protein 1 (ARFRP1). Sys1p is a small integral membrane protein with four predicted transmembrane domains that localises to the Trans Golgi network TGN in yeast and human cells.