SII-SWORD/CoKE huggingface dataset:
Pfam PF22466: PSF3 N-terminal domain (domain)
This entry represents the GINS/PriA/YqbF domain, which is found in the N-terminal region of the GINS complex protein. The GINS complex is crucial for the establishment of DNA replication forks and replisome progression in eukaryotes. The crystal structure of the human GINS complex reveals a heterotetrameric assembly with a pseudo symmetrical layered structure. The complex consists of two heterodimers that create four subunit-subunit interfaces. The subunit structures of the heterodimers consist of two alternating domains, an alpha-helix-rich (A) domain [pfam:PF05916] and a beta-strand-rich (B) domain (this entry).
Pfam PF12844: Helix-turn-helix domain (domain)
Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF18103: Retroviral integrase C-terminal SH3 domain (domain)
This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.
Wikipedia: Retroviral integrase (IN) is an enzyme produced by a retrovirus that integrates its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage integrases (recombinases) used in biotechnology, such as λ phage integrase, as discussed in site-specific recombination.
Pfam PF20791: Acyl-ACP thioesterase C-terminal domain (domain)
This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via  hydrolysing an acyl group on a fatty acid. These proteins are usually composed of a pair of tandem HotDog domains. This entry represents the C-terminal one of the pair.
Pfam PF23956: Family of unknown function (DUF7285) (family)
This entry represents uncharacterised archaeal 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 PF13695: Zinc-binding domain (domain)
This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue.
Pfam PF00950: ABC 3 transport family (family)
Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters are involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two transmembrane regions (TMs), and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment . The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The TMs are bundles of Î± helices that transverse the cytoplasmic membrane multiple times. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Each TM has a prominent cytoplasmic loop which contacts an ABC and represents a conserved motif. The two TMs form either a homodimer (e.g. in the case of the BtuC subunits of the Escherichia coli BtuCD vitamin B12 transporter) , a heterodimer (e.g. the TroC and TroD subunits of the Treponema pallidum general transition metal transporter, TroBCD) , or a pseudo-heterodimer (e.g. the FhuB protein of the E. coli ferrichrome transporter, FhuBC) .
This subfamily consists of integral membrane components from a number of bacterial transport systems that have similar sequences , and include TroC and TroD, and ScaB (required for Mn2+ import in Streptococcus ).
Pfam PF20461: Family of unknown function (DUF6714) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 185 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 PF09910: Uncharacterized protein conserved in archaea (DUF2139) (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 PF03876: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (domain)
Rpb7 bind to Rpb4 to form a heterodimer.  This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation.  This family includes the homologs from RNA polymerase I and III.  In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction.
Pfam PF24586: Domain of unknown function (DUF7611) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to fold into a beta-barrel with a PH-like topology.
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 PF13824: Zinc-finger of mitochondrial splicing suppressor 51 (domain)
Mss51 regulates the expression of cytochrome oxidase, so this domain is probably DNA-binding.
Pfam PF19048: SidE mono-ADP-ribosyltransferase domain (domain)
This domain found in the SidE bacterial effector protein mediates the mono-ADP-ribosylation of ubiquitin, which is then ligated to host proteins by the [pfam:PF12252] domain.
Pfam PF05735: Thrombospondin C-terminal region (family)
This region is found at the C-terminus of thrombospondin  and related proteins.
Pfam PF03196: Protein of unknown function, DUF261 (family)
This is a group of proteins of unknown 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 PF03821: Golgi 4-transmembrane spanning transporter (family)
The lysosome associated protein transmembrane (LAPTM) family is comprised of three members: LAPTM5, LAPTM4a and LAPTM4b; they are lysosome-associated transmembrane proteins, found in mammals, insects and nematodes.
Pfam PF03869: Arc-like DNA binding domain (domain)
Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site.  Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove.
Pfam PF06617: M-phase inducer phosphatase (family)
This family represents a region within eukaryotic M-phase inducer phosphatases ([ec:3.1.3.48]), which also contain the [pfam:PF00581] domain. These proteins are involved in the control of mitosis.
Pfam PF07171: MlrC C-terminus (family)
This family represents the C-terminus (approximately 200 residues) of the product of a bacterial gene cluster that is involved in the degradation of the cyanobacterial toxin microcystin LR. Many members of this family are hypothetical proteins.
Pfam PF11924: Inverse autotransporter, beta-domain (domain)
This is a family of beta-barrel porin-like outer membrane proteins from enteropathogenic Gram-negative bacteria. Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They carry C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal beta domains that are embedded in the outer membrane. This family represents the beta-barrel porin-like domain in the outer membrane that can be found in intimins, invasins and some inverse autotransporters.
Wikipedia: Intimin is a virulence factor (adhesin) of EPEC and EHEC E. coli strains. It is an attaching and effacing (A/E) protein, which with other virulence factors is necessary and responsible for enteropathogenic and enterohaemorrhagic diarrhoea.
Pfam PF04750: FAR-17a/AIG1-like protein (family)
This family includes the hamster androgen-induced FAR-17a protein ([swissprot:Q60534]),  and its human homologue, the AIG1 protein ([swissprot:Q9NVV5]). The function of these proteins is unknown. This family also includes homologous regions from a number of other metazoan proteins.
Pfam PF22993: Ephrin receptor 1 SAM domain-like (domain)
The Ephrin receptor 1 family comprises tyrosine kinase receptors that interact with ephrins and major sperm proteins (MSPs). They play a crucial role in various biological processes including the inhibition of oocyte meiotic maturation and ovulation in the absence of sperm, regulation of somatic cell contraction rates, and modulation of insulin-like signaling pathways through phosphorylation and subsequent degradation of daf-18/PTEN. Additionally, they are involved in morphogenetic events such as head epidermis development, gastrulation, ventral epidermis closure, spermatheca morphogenesis, and axon guidance during neurogenesis.
Pfam PF17240: Family of unknown function (DUF5313) (family)
This is a family of unknown function, found mostly in Actinobacteria and composed of trans-membrane 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 PF09795: Autophagy-related protein 31 (family)
Autophagy is an intracellular degradation system that responds to nutrient starvation.  Cis1/Atg31 has been shown to be required for autophagosome formation in Saccharomyces cerevisiae.  It interacts with Atg17.
Pfam PF04545: Sigma-70, region 4 (domain)
Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Wikipedia: A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).
Pfam PF24767: At5g58720 UBA-like domain (domain)
This domain is found in SMR domain-containing protein At5g58720, Putative nuclear RNA export factor SDE5 from Arabidopsis thaliana and related plant proteins. SDE5 is involved in sense transgene post-transcriptional gene silencing. This domain has detectable similarity to UBA domains, particularly to CUE domain. It is predicted to adopt similar structure composed of alpha-helical bundle.
Pfam PF24267: HVO_1552, C-terminal (domain)
This domain is found at the C-terminal end of the predicted ArsR family transcription regulator HVO_1552 from Haloferax volcanii and similar archaeal sequences. It is predicted to adopt an alpha-helical structure.
Pfam PF09089: Phage short tail fibre protein gp12, middle domain (repeat)
Members of this family adopt a right-handed triple-stranded beta-helix fold, and are found in the middle of the phage short tail fibre protein gp12.
Pfam PF18819: Phage MuF-C-terminal domain (domain)
A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements and also fused to the MuF domain, a structural component of the phage head. The predicted active site contains a conserved histidine and serine residues.
Pfam PF10623: Plasmid conjugative transfer protein PilI (family)
The thin pilus of plasmid R64 belongs to the type IV family and is required for liquid matings.  pilI is one of 14 genes that have been identified as being involved in biogenesis of the R64 thin pilus.
Pfam PF16221: winged helix-turn-helix (domain)
HTH_47 is an example of a circularly permuted winged helix-turn-helix domain. HTH_47 is found at the very C-terminus of DUF2172, which is structurally similar to M28-peptidases but lacking one of the key zinc-binding residues.
Pfam PF06988: NifT/FixU protein (family)
This family consists of several NifT/FixU bacterial proteins. NifT/FixU is a very small, conserved protein that is found in nif clusters; however, its function is unknown. Although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in K. pneumoniae has only a limited effect on nitrogen fixation.
Pfam PF15655: NTF2 fold immunity protein (family)
A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-JAB-2 family.
Pfam PF17796: Major Vault Protein repeat domain (domain)
This domain is found in the major vault protein.
The major vault protein is the major polypeptide component of a large cellular ribonuclear protein complex found in the cytoplasm of eukaryotic cells (known as vaults). Several roles for vaults have been proposed. Vault proteins have been associated with development of multi-drug resistance . They have also being implicated in the regulation of several cellular processes including transport mechanisms, signal transmission and immune responses .
Pfam PF19892: Family of unknown function (DUF6365) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001960) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the hiroshidine biosynthetic gene cluster from Streptomyces hiroshimensis.
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 PF01472: PUA domain (family)
The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes.  It is predicted that the PUA domain is an RNA binding domain.
Pfam PF09123: Domain of unknown function (DUF1931) (domain)
Members of this family, which are found in a set of hypothetical bacterial proteins, contain a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined. The known structure shows this domain contains two copies of the histone 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 PF11432: Protein of unknown function (DUF3197) (family)
This bacterial family of 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 PF24680: Hsr-9 Tudor domain (domain)
This entry represents the tandem Tudor domains of Hsr-9 from C. elegans and similar nematode proteins. Hsr-9 may have a role in DNA double-strand break repair following gamma-irradiation.
Pfam PF04352: ProQ/FINO family (domain)
This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProP, in Escherichia coli. This family includes several bacterial fertility inhibition (FINO) proteins. The conjugative transfer of F-like plasmids is repressed by FinO, an RNA binding protein. FinO interacts with the F-plasmid encoded traJ mRNA and its antisense RNA, FinP, stabilising FinP against endonucleolytic degradation and facilitating sense-antisense RNA recognition. ProQ operates as an RNA-chaperone, binding RNA and bringing about both RNA strand-exchange and RNA duplexing. This suggests that in fact it does not regulate ProP transcription but rather regulates ProP translation through activity as an RNA-binding protein.
Pfam PF01562: Reprolysin family propeptide (family)
This region is the propeptide for members of peptidase family M12B.  The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.
Pfam PF14575: Ephrin type-A receptor 2 transmembrane domain (domain)
Epha2_TM represents the left-handed dimer transmembrane domain of of EphA2 receptor.  This domain oligomerises and is important for the active signalling process.
Pfam PF15823: UPF0524 of C3orf70 (family)
UPF0524 is a family of proteins found in eukaryotes. Proteins in this family are typically between 183 and 250 amino acids in length. The function is not known.
Pfam PF02537: CrcB-like protein, Camphor Resistance (CrcB) (family)
CRCB is a family of bacterial integral membrane proteins with four TMs.. Over expression in E. coli also leads to camphor resistance.
Pfam PF11806: Enterochelin esterase, N-terminal (domain)
This entry represents the N-terminal domain of enterochelin esterase. The activity of the enzyme has been characterised. Fes catalyses the hydrolysis of the 2,3-dihydroxy-N- benzoyl-L-serine trimer, enterochelin, forming 2,3- dihydroxybenzoylserine. It also catalyses hydrolysis of free enterobactin and ferric enterobactin. Upon hydrolysis of ferric enterobactin by Fes, released iron is probably reduced by a second enzyme. Enterochelin esterase represents a family of non-peptidase homologues belonging to the MEROPS peptidase family S9, clan SC.
Pfam PF03810: Importin-beta N-terminal domain (repeat)
This entry represents the N-terminal domain of importin-beta (also known as karyopherins-beta) that is important for the binding of the Ran GTPase protein .
Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins , which is important for importin-beta mediated transport.

Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released . There are additional release factors as well.
Wikipedia: Importin is a type of karyopherin that transports protein molecules from the cell's cytoplasm to the nucleus. It does so by binding to specific recognition sequences, called nuclear localization sequences (NLS).
Pfam PF14461: Prokaryotic E2 family B (family)
A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are  similar to the eukaryotic E2 proteins but lack the conserved asparagine. Members of this family are usually fused to an E1 domain at the C-terminus. The protein is usually in the gene neighborhood of a gene encoding  a member of the pol-beta nucleotidyltransferase superfamily. Many of the operons in this family are in ICE-like mobile elements and plasmids.
Pfam PF12410: Poxvirus DNA dependent RNA polymerase 30kDa subunit (family)
This family of proteins is found in viruses. Proteins in this family are typically between 193 and 259 amino acids in length. The family is found in association with [pfam:PF01096]. There are two conserved sequence motifs: GIEYSKD and LRY. This family is N terminal of the 30 kDa subunit of poxvirus DNA-d-RNA-pol. It has structural similarity to the eukaryotic transcriptional elongation factor SII.