SII-SWORD/CoKE huggingface dataset:
Pfam PF10524: Nuclear factor I protein pre-N-terminus (family)
The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organisms. The N-terminal 200 residues contains the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication.
Pfam PF06326: Vesiculovirus matrix protein (family)
This family consists of several Vesiculovirus matrix proteins. The matrix (M) protein of vesicular stomatitis virus (VSV) expressed in the absence of other viral components causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein.
Wikipedia: The family of vesiculovirus matrix proteins consists of several matrix proteins of the vesicular stomatitis virus, also known as VSIV or VSV. The matrix (M) protein of the virus causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein.
Pfam PF25059: DSCAM/DSCAML C-terminal Ig-like domain (domain)
This entry represents an Ig-like domain found at the C-terminal of DSCAM and DSCAML  molecules. DSCAM and DSCAML are cell adhesion molecules that play a role in neuronal self-avoidance. They promote repulsion between specific neuronal processes of either the same cell or the same subtype of cells.
Pfam PF02102: Deuterolysin metalloprotease (M35) family (family)
This group of metallopeptidases belong to MEROPS peptidase family M35 (deuterolysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.

Deuterolysin is a microbial zinc-containing metalloprotease that shows some similarity to thermolysin . The protein is expressed with a possible 19-residue signal sequence, a 155-residue propeptide, and an active peptide of 177 residues . The latter contains an HEXXH motif towards the C terminus, but the other zinc ligands are as yet undetermined .
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
Pfam PF03644: Glycosyl hydrolase family 85 (family)
Family of endo-beta-N-acetylglucosaminidases.  These enzymes work on a broad spectrum of substrates.
Wikipedia: In molecular biology, glycoside hydrolase family 85 is a family of glycoside hydrolases.
Pfam PF05935: Arylsulfotransferase (ASST) (repeat)
This family consists of several bacterial Arylsulfotransferase proteins. Arylsulfotransferase (ASST) transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate.
Wikipedia: An aryl sulfotransferase is an enzyme that 
transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate.3'-phosphoadenylyl sulfate + a phenol  adenosine 3',5'-bisphosphate + an aryl sulfate
Pfam PF14635: Helix-hairpin-helix motif (domain)
This entry represents a helix-hairpin-helix motif found in the transcription elongation factor Spt6 . Spt6 is involved in the regulation of histone modification .
Pfam PF04719: hTAFII28-like protein conserved region (domain)
The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex.  The conserved region is found at the C-terminal of most member proteins.  The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits.  The conserved region contains four alpha helices and three loops arranged as in histone H3.
Wikipedia: Transcription initiation factor TFIID subunit 11 also known as TAFII28, is a protein that in humans is encoded by the TAF11 gene.
Pfam PF12026: Crk-Associated Substrate C-terminal domain (domain)
This is a C-terminal domain found in CAS family members. The CAS (Crk-Associated Substrate) protein family is a group of scaffolding proteins that play important modulatory roles in both normal and pathological cell growth regulation. They contain an N-terminal Src homology 3 (SH3) domain [pfam:PF00018] and a substrate domain (SD). The SD contains a large number of YxxP motifs, which when phosphorylated by Src-family kinases provide canonical binding sites for proteins containing SH2 domains such as Crk, Crk-L, CRKII presumed domain is functionally uncharacterised.
Pfam PF13076: Fur-regulated basic protein A (family)
This family of proteins is regulated by the ferric uptake regulator protein Fur. This family does not regulate the lutABC operon encoding iron sulfur-containing enzymes necessary for growth on lactate.
Pfam PF15594: Immunity protein 50 (family)
A predicted immunity protein with an all-beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-HHH or Ntox24 families.
Pfam PF04652: Vta1 like (family)
Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4.  Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT).  Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region.
Pfam PF21194: TadZ-like, receiver domain (domain)
This domain is found at the N-terminal of TadZ from Eubacterium rectale and similar bacterial proteins. TadZ is is an essential component of the Tad secretion system that probably functions as a localization factor. This protein is composed of two domains, both of which have lost its active sites. This entry represents the N-terminal atypical receiver domain (ARD), which is structurally similar to the RD of response regulators such as the chemotaxis protein CheY.
Pfam PF24208: Endo-acting ulvan lyase beta-trefoil domain (domain)
This entry represents the beta-trefoil domain found in endo-acting ulvan lyase from bacteria. Ulvan lyases degrade the main polysaccharide component of green seaweed cell walls. This domain binds to ulvan.
Pfam PF16705: NUDIX, or N-terminal NPxY motif-rich, region of KRIT (domain)
NUDIX_5 is found in higher eukaryotes at the N-terminus of KRIT1 or Krev interaction trapped proteins. NUDIX_5 carries three NPxY-like motifs, and it is found to bind the integrin cytoplasmic-associated protein 1 ICAP1. In the absence of KRIT1 ICAP1 binds via its C-terminal PH/PTB fold domain to the integrin beta-1 cytoplasmic tail. Binding of KRIT1 to ICAP1 via NUDIX_5 out-competes the binding of ICAP1 to integrin cytoplasmic tails such that ICAP1 is sequestered in the nucleus. Integrin activation is thus prevented.
Pfam PF17281: Family of unknown function (DUF5346) (family)
This family of unknown function is found in Nematoda.
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 PF10973: Protein of unknown function (DUF2799) (family)
Some members in this family of proteins are annotated as yfiL which 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 PF13719: zinc-ribbon domain (domain)
This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, [pfam:PF12773].
Pfam PF04448: Protein of unknown function (DUF551) (family)
This family represents the carboxy terminus of a protein of unknown  function, found in dsDNA viruses with no RNA stage, including  bacteriophages lambda and P22, and also in some Escherichia coli prophages.
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 PF08863: YolD-like protein (domain)
Members of this family are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from gram-negative bacteria. This family has been shown to belong to the WYL-like superfamily.
Pfam PF08523: Multiprotein bridging factor 1 (family)
This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2.  It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC.  The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif ([pfam:PF01381]) is found to its C-terminus.
Pfam PF05179: RNA pol II accessory factor, Cdc73 family, C-terminal (domain)
CDC73 is an RNA polymerase II accessory factor, and forms part of the Paf1 complex that has roles in post-initiation events.  More specifically, crystal structure analysis shows the C-terminus to be a Ras-like domain that adopts a fold that is highly similar to GTPases of the Ras superfamily. The canonical nucleotide binding pocket is altered in CDC73, and there is no nucleotide ligand, but it contributes to histone methylation and Paf1C recruitment to active genes. Thus together with Rtf1 it combines to couple the Paf1 complex to elongating polymerase. The family has been added to the P-loop clan on the basis of the topology of the b-stranded core, and its similarity to Ras.
Pfam PF08088: Conotoxin I-superfamily (family)
This family consists of the I-superfamily of  conotoxins. This is a new class of peptides in  the venom of some Conus species. These toxins  are characterised by four disulfide bridges and inhibit of modify ion channels of nerve cells.  The I-superfamily conotoxins is found in five or  six major clades of cone snails and could possible  be found in many more species.
Pfam PF11912: Counting factor-associated protein A/B/C (family)
Developing Dictyostelium (Slime mold) cells form large aggregation streams that break up into groups of cells. Each group then becomes a fruiting body. Cells sense if there are too many cells in a stream by sensing the concentration of counting factor (CF), a protein complex secreted by the aggregating cells. This entry includes counting factor-associated protein A/B/C from Slime mold.
Pfam PF21848: Domain of unknown function (DUF6907) (domain)
This entry represents a family of Actinobacterial proteins of unknown function. AlphaFold predicts a confident dimeric arrangement. This family appears to be distantly related to [pfam:PF19887].
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 PF10737: Spore germination protein GerPC (family)
GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor.
Pfam PF14279: HNH endonuclease (domain)
This domain is related to other HNH domain families such as [pfam:PF01844]. Suggesting that these proteins have a nucleic acid cleaving function.
Pfam PF15750: Ubiquitin-binding zinc-finger (family)
This domain is the ubiquitin-binding zinc-finger of the Fanconi anaemia-associated protein of 20 kDa.
Pfam PF22048: LSO1/2-like (family)
This family includes Protein LSO1/2 from Saccharomyces cerevisiae and similar sequences mainly found in fungi. LSO1 is likely to play a role in iron homeostasis. Its paralogue LSO2, which is constitutively expressed, is a ribosome-associated protein required for translational recovery after starvation from stationary phase. LSO2 is an orthologue of Coiled-coil domain containing 124 (CCDC124, see [pfam:PF06244]).
Pfam PF05389: Negative regulator of genetic competence (MecA) (family)
This family contains several bacterial MecA proteins. The development of competence in Bacillus subtilis is regulated by growth conditions and several regulatory genes. In complex media competence development is poor, and there is little or no expression of late competence genes. Mec  mutations permit competence development and late competence gene expression in complex media, bypassing the requirements for many of the competence regulatory genes. The mecA gene product acts negatively in the development of competence. Null mutations in mecA allow expression of a late competence gene comG, under conditions where it is not normally expressed, including in complex media and in cells mutant for several competence regulatory genes. Overexpression of MecA inhibits comG transcription.
Pfam PF11335: Protein of unknown function (DUF3137) (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 PF16934: Two-component Enterococcus faecalis cytolysin (EFC) (domain)
Mersacidin is a cytolysin, a lantibiotic produced by Gram-positive bacteria, The cytolysin is a 'pseudohaemolysin' which produces haemolysis on blood agar plates, but not in broth culture. Mersacidin is one of the type B lantibiotics (lanthionine-containing antibiotics) that contain post-translationally modified amino acids and cyclic ring structures.  Mersacidin attacks the cell wall precursor lipid II, thereby inhibiting cell-wall synthesis.
Pfam PF07990: Nucleic acid binding protein NABP (domain)
Many members of this family are putative nucleic acid binding proteins. One member of this family has been partially characterised and  contains two putative phosphorylation sites and a possible dimerisation  / leucine zipper domain.
Pfam PF16346: GH32, BT1760-like, C-terminal domain (domain)
This domain is found at the C-terminal end of BT1760 from Bacteroides thetaiotaomicron and similar bacterial proteins that predominantly belong to the glycoside hydrolase family 32 (GH32). BT1760 is an endo-levanase that requires its C-terminal beta-sandwich domain to fold and function correctly. This domain shows two facing beta-sheets consisting of seven and eight antiparallel beta-strands.
Pfam PF02301: HORMA domain (domain)
The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.
Wikipedia: In molecular biology, the HORMA domain is a protein domain that has been suggested to recognise chromatin states resulting from DNA adducts, double stranded breaks or non-attachment to the spindle and act as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.
Pfam PF19422: Ariadne domain (domain)
This entry represents the Ariadne domain found in the Ariadne subfamily E3 ubiquitin ligase proteins. The C-terminal Ariadne domain adopts an elongated four-helix bundle consisting of an antiparallel arrangement of seven-to-ten-turn long helices. The Ariadne domain is straddled on one side by the IBR domain, and on the other by the RING2 domain. Notably, the Ariadne domain embraces the surface of RING2 containing the catalytic Cys357. The ariadne Domain Masks the HHARI Catalytic Cys357 and Inhibits Intrinsic E3 Activity.
Pfam PF16703: Domain of unknown function (DUF5064) (domain)
This is found in Pseudomonas species. Several members are annotated as being acetyl-CoA carboxylase alpha subunit, but his could not be confirmed.
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 PF20042: Family of unknown function (DUF6444) (family)
This entry represents a region that is sometimes found a the N-terminus of transposon proteins. It is also sometimes found as part of a shorter protein, presumably involved in transposition.
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 PF22348: Colicin-A N-terminal domain (domain)
This entry represents the N-terminal translocation domain of colicin A, an endonuclease active on both single- and double-stranded DNA but with undefined specificity. This domain interacts directly with TolAIII (C-terminal domain of TolA) which facilitates translocation through the cell envelope to reach their cytotoxic site of action.
Pfam PF07311: Dodecin (family)
Dodecin is a flavin-binding protein,found in several bacteria and  few archaea and represents a stand-alone version of the SHS2  domain. It most closely resembles the SHS2 domains of FtsA and  Rpb7p, and represents a single domain small-molecule binding form.
Pfam PF05489: Phage Tail Protein X (domain)
This domain is found in a family of phage tail proteins. Visual analysis suggests that it is related to [pfam:PF01476] (personal obs: C Yeats). The functional annotation of family members further confirms this hypothesis.
Pfam PF00384: Molybdopterin oxidoreductase (domain)
This domain is found in a number of molybdopterin-containing oxidoreductases, tungsten formylmethanofuran dehydrogenase subunit d (FwdD), and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where a single domain constitutes almost the entire subunit. This domain is also found in periplasmic nitrate reductases, trimethylamine-N-oxide reductases, dimethyl sulfoxide reductase DmsA among other dehydrogenases/reductases. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor .
Pfam PF03106: WRKY DNA -binding domain (domain)
The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding . Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene.

Structural studies indicate that this domain is a four-stranded Î²-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure . The WRKYGQK residues correspond to the most N-terminal Î²-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the Î²-sheet.
Wikipedia: The WRKY domain is found in the WRKY transcription factor family, a class of transcription factors. The WRKY domain is found almost exclusively in plants although WRKY genes appear present in some diplomonads, social amoebae and other amoebozoa, and fungi incertae sedis. They appear absent in other non-plant species. WRKY transcription factors have been a significant area of plant research for the past 20 years. The WRKY DNA-binding domain recognizes the W-box (T)TGAC(C/T) cis-regulatory element.
Pfam PF06475: Putative glycolipid-binding (domain)
This family has a novel fold known as a spiral beta-roll, consisting of a 15-stranded beta sheet wrapped around a single alpha helix. It forms dimers. It has some structural similarity to the E. coli lipoprotein localisation factors LolA, [swissprot:P61316] and LolB, [swissprot:P61320]. Its structure suggests that it may have a role in glycolipid binding. Its genomic context supports a role in glycolipid metabolism.