SII-SWORD/CoKE huggingface dataset:
Pfam PF03857: Colicin immunity protein (family)
Colicin immunity proteins are plasmid-encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress.
Pfam PF05764: YL1 nuclear protein (family)
The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor.
Pfam PF13765: SPRY-associated domain (domain)
PRY is a 50-60 amino acids domain associated with SPRY domains, adjacent to its N-terminal. PRY and SPRY domains are structurally very similar and consist of a beta sandwich fold. Distant  homologues are domains in butyrophilin/marenostrin/pyrin, evolutionarily more ancient than SPRY/B30.2 counterpart.
Pfam PF17351: Family of unknown function (DUF5380) (family)
This is a family of unknown function found in Rhabditida.
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 PF13002: Arrestin_N terminal like (family)
This is a family of proteins related to the Arrestin_N terminal family.
Pfam PF20466: MmeI, target recognition domain (domain)
Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues  301-320) via a multi-helical spacer (residues 156-300).  These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major  groove, while the MTase domain makes several contacts to the DNA  in the minor groove. This domain corresponds to the TRD. It consists of two  alpha/beta subdomains.
Pfam PF24250: Transcription regulator HVO_2718-like (family)
This is a family of archaeal transcription regulators, including HVO_2718 from Haloferax volcanii. Members of this family are predicted to show an HTH fold towards the C-terminal end.
Pfam PF17815: PDZ domain (domain)
This entry contains the second PDZ domain from plant peptidases such as Deg2. This domain is involved in cage assembly.
Pfam PF14067: LssY C-terminus (family)
This domain is found at the C-terminus of Legionella LssY proteins, which may be a part of the type I secretion system. This domain is functionally uncharacterised. This domain is found in bacteria, and is typically between 182 and 195 amino acids in length. It is often found in association with [pfam:PF09335] and PF01569. There are two completely conserved residues (P and W) that may be functionally important.
Pfam PF03545: Yersinia virulence determinant (YopE) (family)
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia .

The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself , type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.

Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason . Yersinia secrete a Rho GTPase-activating protein, YopE , that disrupts the host cell actin cytoskeleton. YopE is regulated by another bacterial gene, SycE , that enables the exotoxin to remain soluble in the bacterial cytoplasm. A similar protein, exoenzyme S (ExoS) from Pseudomonas aeruginosa, has both ADP-ribosylation and GTPase activity .

This entry refers to the GTPase-activating protein (GAP) domain found in YopE, ExoS, and also SptP (Secreted effector protein) .
Wikipedia: In molecular biology, the protein domain YopE refers to the secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. It not only infects the host cell but also protects the bacteria. It undergoes several mechanisms to evade the host's immune system. This particular protein domain can be referred to as a Rho GTPase-activating protein (GAP).
Pfam PF07685: CobB/CobQ-like glutamine amidotransferase domain (domain)
This group of enzymes was suggested to be related to the MinD family of ATPases involved in regulation of cell division in bacteria and archaea . Further sequence analysis suggests a model for the interaction of CobB and CobQ with their respective substrates . CobB and CobQ were also found to contain unusual Triad family (class I) glutamine amidotransferase domains with conserved Cys and His residues, but lacking the Glu residue of the catalytic triad .
Pfam PF10253: Mitotic checkpoint regulator, MAD2B-interacting (family)
This family constitutes the major, conserved, portion of PRCC proteins. In humans this family interacts with MAD2B, the mitotic checkpoint protein. In Schizosaccharomyces pombe this protein is part of the Cwf-complex that is known to be involved in pre-mRNA splicing.
Pfam PF11628: T-cell surface glycoprotein CD3 zeta chain (family)
The incorporation of the zetazeta signalling module requires one basic TCR alpha and two zetazeta aspartic acid TM residues. The structure of the zetazeta(TM) dimer consists of a left-handed coiled coil with polar contacts. Two aspartic acids are critical for zetazeta dimerisation and assembly with TCR.
Wikipedia: The T-cell receptor (TCR) is a protein complex found on the surface of T cells, or T lymphocytes, that is responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules. The binding between TCR and antigen peptides is of relatively low affinity and is degenerate: that is, many TCRs recognize the same antigen peptide and many antigen peptides are recognized by the same TCR.
Pfam PF07764: Omega Transcriptional Repressor (domain)
The omega transcriptional repressor regulates expression of involved in copy number control and stable maintenance of plasmids. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA.
Pfam PF01171: PP-loop family (family)
This family of proteins belongs to the PP-loop superfamily.
Pfam PF13938: Putative heavy-metal chelation (family)
This domain of unknown function has an enolase N-terminal domain-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the N-terminus of proteins containing DUF364, [pfam:PF04016].  The structure of UnioProtKB:B8FUJ5, PDB:3l5o, suggests that the whole protein has this enolase N-terminal-like fold and an Rossmann-like C-terminal domain.  Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The protein may be playing a role in heavy-metal chelation.
Pfam PF20812: Bacteriophage PM2, Viral membrane protein P3 (domain)
Viral membrane protein P3 assemblies into dimers. Each P3 subunit comprise a core of two perpendicular alpha    helices, and subunits are bound together by a parallel two-stranded beta sheet. 120 asymmetric dimers form a layer below the outer capsid shell in an almost planar structure. This protein family is found in Bacteriophage PM2 and similar PRD1-adenovirus.
Pfam PF15726: Domain of unknown function (DUF4677) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 195 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 PF20335: Domain of unknown function (DUF6630) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 270 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 PF02713: Domain of unknown function DUF220 (family)
This is family consists of a region in several Arabidopsis thaliana hypothetical proteins none of which have any known function. The aligned region contains two cysteine residues. This domain shows structural similarity to members of the Bet v1-like superfamily and may be involved in lipid binding.
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 PF18108: QSOX Trx-like domain (domain)
This domain is found in Quiescin sulfhydryl oxidase (QSOX), an oxidoreductase present in Homo sapiens capable of both generating and transferring disulfide modules within a single polypeptide. The domain is thioredoxin-like, hence referred to as Trx1 domain. Trx1 domain has a di-cysteine motif (Cys-X-X-Cys) which is related to the redox-active domains of protein disulfide isomerase. The Trx1 domain is responsible for intramolecular disulfide transfer through the di-cysteine motif.
Pfam PF11115: Protein of unknown function (DUF2623) (family)
This family is conserved in the Enterobacteriaceae family. Several members are named as YghW. The function is not known.
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 PF07068: Major capsid protein Gp23 (family)
This family contains a number of major capsid Gp23 proteins approximately 500 residues long, from T4-like bacteriophages.
Pfam PF12057: BCL2-associated athanogene 6 (domain)
This domain is found in large proline-rich protein BAG6 protein. It has a conserved SDL sequence motif. Human BAG6 is an ATP-independent molecular chaperone preventing the aggregation of misfolded and hydrophobic patches-containing proteins. It functions as part of a cytosolic protein quality control complex, the BAG6/BAT3 complex, which maintains these client proteins in a soluble state and participates to their proper delivery to the endoplasmic reticulum or alternatively can promote their sorting to the proteasome where they undergo degradation.
Pfam PF14554: VEGF heparin-binding domain (domain)
This short domain is found at the C-terminus of VEGF. It has been shown to have heparin binding activity.
Pfam PF07800: Protein of unknown function (DUF1644) (family)
This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, and is probably a zinc-binding domain.
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 PF03630: Fumble (family)
Fumble is required for cell division in Drosophila.  Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with  high similarity to the pantothenate kinases of A. nidulans and mouse. A role of fumble in membrane synthesis has been proposed.
Pfam PF17738: DUF5575 central RNaseH like domain (domain)
This entry represents the central domain from a family of Chordate proteins that includes C19orf68. These proteins appear to be transposon related. This domain appears to be closely related to the MULE RNaseH domain [pfam:PF10551].
Pfam PF22916: UTP25, NTP hydrolase-like domain (domain)
UTP25 (U3 small nucleolar RNA-associated protein 25) is a a DEAD-box RNA helicase-like protein component of the ribosomal small subunit processome for the biogenesis of ribosomes, which functions in pre-ribosomal RNA (pre-rRNA) processing. U3 small nucleolar RNA-associated protein 25 homologue (also known as Digestive organ expansion factor (DEF)) from animals is essential for embryonic development in part through the regulation of p53 pathway and controls the expansion growth of digestive organs and liver. UTP25 mediates, with CAPN3, the proteasome-independent degradation of p53/TP53. These proteins display limited sequence similarity to DEAD-box RNA helicases, having alternative residues at the Walker A and DEAD-box sites, but conservation of structural and other key residues. They consist of two domains; this entry represents the bigger one, towards the N-terminal which is structurally related to NTPases, lacking the conserved motifs typically found in helicases (WalkerA/B motifs and motif Q). The C-terminal domain is represented in [pfam:PF06862]. This domain is required and sufficient for the interaction of Utp25 with Utp3. UTP25 interacts with nucleolar protein Nop19 in S. cerevisiae, and Nop19p is essential for the incorporation of Utp25p into pre-ribosomes.
Pfam PF15284: Phage-encoded virulence factor (family)
PAGK represents a new of virulence factors that is translocated into the host cytoplasm via bacterial outer membrane vesicles (OMV). Members are small proteins composed of ~70 amino acids. In Salmonella they are secreted independently of the SPI-2 type-III secretion system, T3SS. The OMV functions as a vehicle for transferring virulence determinants to the cytoplasm of the infected host cell. OMVs are released from the cell envelopes of Gram-negative bacteria and comprise a variety of outer membrane and periplasmic constituents, including proteins, phospholipids, lipopolysaccharides, and DNA.
Pfam PF14521: Lysine-specific metallo-endopeptidase (domain)
This is the catalytic region of aspzincins, a group of lysine-specific metallo-endopeptidases in the MEROPS:M35 family. They exhibit the following active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs. In UniProt:P81054, His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner.
Pfam PF07985: SRR1 domain (domain)
SRR1 proteins are signalling proteins involved in regulating the circadian clock in Arabidopsis. This presumed domain has a Rossmann-like fold and structural models suggest it may have a methyltransferase function.
Pfam PF04056: Ssl1-like (family)
Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
Pfam PF17203: Single cache domain 3 (domain)
This domain is associated to sensor histidine kinases and recognises citrate and TCA cycle intermediates, Ag(II), Zn(II), Mg(II) (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: In molecular biology, the cache domain is an extracellular protein domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria such as Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions.
Pfam PF24353: Domain of unknown function (DUF7513) (domain)
This domain is found in uncharacterised proteins from Halobacteria. It has a detectable sequence similarity to TRAM domains and it is predicted to adopt a similar structure. It is found as standalone domain.
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 PF02088: Ornatin (family)
Ornatin is a potent glycoprotein IIb-IIIa (GP IIb-IIIa) antagonist and platelet aggregation inhibitor . The protein is 41-52 residues in length and contains the RGD recognition motif common in adhesion proteins, and 6 conserved cysteine residues. The sequences of ornatin isoforms B, C, D and E are highly similar, while isoforms A2 and A3 are less similar, lacking the N-terminal 9 residues. Ornatins share ~40% identity with decorsin, a GP IIb-IIIa antagonist isolated from the leech (Macrobdella decora) .
Pfam PF13751: Transposase DDE domain (domain)
Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.
Pfam PF04993: TfoX N-terminal domain (domain)
TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes. This family corresponds to the N-terminal presumed domain of TfoX. The domain is found as an isolated domain in some proteins suggesting this is an autonomous domain.
Pfam PF24562: MRC2-like, N-terminal cysteine-rich domain (domain)
This cysteine-rich domain is found at the N-terminal end of human C-type mannose receptor 2 (MRC2) and similar proteins from vertebrates. MRC2 internalises glycosylated ligands from the extracellular space for release in an endosomal compartment and may play a role as endocytotic lectin receptor. It may also be involved in cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. This domain is organised into two regions: the N-terminal folds into two lobes similarly to the canonical beta-trefoil structure. The predicted third lobe folds into an alpha-helix followed by a long flexible loop and a beta-strand.
Pfam PF06813: Nodulin-like (domain)
This entry represents a conserved domain within plant nodulin-like proteins. Including this domain is the Arabidopsis thaliana protein  NFD4 (Nuclear Fusion Defective 4). NFD4 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus.
Pfam PF10382: DNA helicase ZGRF1-like, N-terminal domain (domain)
This domain can be found in human 5'-3' DNA helicase ZGRF1 and similar eukaryotic proteins. ZGRF1 promotes repair of replication -blocking DNA lesions through stimulation of homologous recombination (HR). This domain can also be found in Mte1 (Mph1-associated telomere maintenance protein 1) from Saccharomyces cerevisiae, which is involved in telomere maintenance and in and fission yeast Dbl2, involved in meiotic chromosome segregation. However, there is no evidence to suggest that this domain, which is predicted to adopt an all-beta structure, is implicated in DNA damage resistance or nuclear focus formation.
Pfam PF17227: Family of unknown function (DUF5302) (family)
Family of unknown function found in Actinobacteria with highly conserved motif of FRRKSG found at the C-terminus.
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 PF20463: Prephenate dehydrogenase, dimerization domain (domain)
Members of this family are prephenate dehydrogenases [ec:1.3.1.12] (PDHs) involved in tyrosine biosynthesis. This is the C-terminal, helical dimerization domain of PDHs.
Pfam PF10205: Predicted coiled-coil domain-containing protein (coiled_coil)
This is the N-terminal 100 amino acid domain of a family of proteins conserved from nematodes to humans. It carries a characteristic KLRAQ sequence-motif. The function is not known.