SII-SWORD/CoKE huggingface dataset:
Pfam PF19493: Trypsin-co-occurring domain 1 (domain)
Trypsin-like peptidase effector in the classical NTP-dependent ternary system (vWA-MoxR-VMAP) frequently co-occurs with one of two proteins (Trypco1 or Trypco2) which are mostly mutually exclusively.  This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the  kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus.
Pfam PF16264: SatD family (SatD) (family)
This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Streptococcus species. The function of this family is involved in acid resistance.
Pfam PF18182: minimal CRISPR polymerase domain (domain)
Minimal version of the CRISPR polymerase domain. Predicted to generate cyclic nucleotides, potentially sensed by CARF domains which in turn activate various effector domain including HEPN RNases, CARF sensor and effectors are found in conserved genome contexts. Part of a broader class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Implicates CRISPR polymerase of the Type III CRISPR/Cas systems in a nucleotide synthetase functional role.
Pfam PF21221: Metallo-beta-lactamase-like, C-terminal domain (domain)
This domain is found in Metallo-beta-lactamase family protein from Thermus thermophilus (TTHA1429) and similar bacterial enzymes. This domain is often found C-terminal to [pfam:PF00753].
Pfam PF05385: Mastadenovirus early E4 13 kDa protein (family)
This family consists of human and simian mastadenovirus early E4 13 kDa proteins. Human adenovirus type 9 (Ad9) is unique in eliciting exclusively estrogen-dependent mammary tumours in rats and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9.
Pfam PF07364: Metallopeptidase family M81 (domain)
This is a family of proteobacterial metallo-peptidases.
Pfam PF17587: Discriminator of mRNA degradation (family)
This family includes Dmd peptides from T4 phages. Dmd can suppress the toxicities of toxins such as LsoA (an endoribonucleases toxin expressed by E.coli). Crystal structure analysis show that Dmd is inserted into the deep groove between the N-terminal repeated domain (NRD) and the Dmd-binding domain (DBD) of LsoA. Site-directed mutagenesis of Dmd revealed the conserved residues (W31 and N40) are necessary for LsoA binding and the toxicity suppression.
Pfam PF16806: Antiactivator protein ExsD N-terminal domain (domain)
The antiactivator protein ExsD represses the transcriptional activator ExsA. ExsA activates expression of type III secretion system genes. Repression of ExsA by ExsD is relieved by the secretion chaperone ExsC.
Pfam PF24279: HVO_2525, N-terminal (domain)
This domain is found at the N-terminal of the predicted transcription regulator HVO_25253 from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an alpha-beta structure. It is often found associated with [pfam:PF04967].
Pfam PF12134: PRP8 domain IV core (domain)
This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with [pfam:PF10597], [pfam:PF10596], [pfam:PF10598], [pfam:PF08083], [pfam:PF08082], [pfam:PF01398], [pfam:PF08084]. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core.
Pfam PF01928: CYTH domain (domain)
These sequences are functionally identified as members of the adenylate cyclase family, which catalyses the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate.  Six distinct non-homologous classes of AC have been identified.  The structure of three classes of adenylyl cyclases have been solved.
Pfam PF05510: Sarcoglycan alpha/epsilon N-terminal domain (domain)
Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear. This family contains alpha and epsilon members. This entry represents the N-terminal domain.
Wikipedia: The sarcoglycans are a family of transmembrane proteins involved in the protein complex responsible for connecting the muscle fibre cytoskeleton to the extracellular matrix, preventing damage to the muscle fibre sarcolemma through shearing forces.
Pfam PF08455: Bacterial SNF2 helicase associated (family)
This domain is found in bacterial proteins of the SWF/SNF/SWI helicase family to the N-terminus of the SNF2 family N-terminal domain ([pfam:PF00176]) and together with the Helicase conserved C-terminal domain ([pfam:PF00271]). The function of the domain is not clear.
Pfam PF02785: Biotin carboxylase C-terminal domain (domain)
Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in  this C-terminal domain.
Wikipedia: In enzymology, a biotin carboxylase (EC 6.3.4.14) is an enzyme that catalyzes the chemical reactionATP + biotin-carboxyl-carrier protein + CO2  ADP + phosphate + carboxybiotin-carboxyl-carrier protein
Pfam PF18891: FANCL UBC-like domain 3 (domain)
This entry represents the third of three UBC-like domain found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2.
Pfam PF22114: Nucleoporin NUP120, helical domain (domain)
This domain is found in Nucleoporin NUP120 from Saccharomyces cerevisiae and similar fungal sequences. NUP120 is a a component of the nuclear pore complex (NPC) involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organisation. This entry represents the alpha-helical domain of NUP120, which packs against the side of the beta-propeller [pfam:PF11715], located N-terminal of the protein.
Pfam PF20887: PWWP domain-containing DNA repair factor 3A/B, N-terminal (domain)
PWWP domain-containing DNA repair factor 3A (also known as EXPAND1 or MUM1) is a nucleosome-binding protein that contributes to the maintenance of chromatin state. Through its interaction with 53BP1, it serves as an accessory factor in the DNA damage response pathway to promote chromatin change in response to DNA damage. MUM1 promotes cell survival following DNA damage, suggesting that it may facilitate DNA repair by regulating the organisation of chromatin structure. This is the N-terminal domain from PWWP domain-containing DNA repair factors 3A/B, which shows similarities to chromodomains and may function as a histone reader.
Pfam PF03994: Domain of Unknown Function (DUF350) (repeat)
This entry represents a family of bacterial proteins that form an integral membrane protein complex. These complexes form an alpha/alpha(8) structure. These proteins are composed of repeats of a two TM helix motif. The function of these proteins is currently unknown.
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 PF19540: Family of unknown function (DUF6064) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 215 and 242 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 PF20924: RLIP76, Ral binding domain (domain)
This domain is found in RLIP76 (also known as RalA-binding protein 1, RalBP1), a multifunctional protein that interacts with multiple small G protein families and endocytosis proteins. The Ral binding domain is a coiled-coil. The orientation of its alpha-helices and the loop between them slightly changes upon binding to RalB. This interaction appears to be related to the cellular localization of the complex.
Pfam PF03604: DNA directed RNA polymerase, 7 kDa subunit (domain)
This family includes the DNA-directed RNA polymerases I, II, and III subunit RPABC4 (also known as RPC10 and ABC10-alpha)  and archaeal polymerase subunit P .
DNA-directed RNA polymerases 2.7.7.6 (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:


 * RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.
 * RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.
 * RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.


Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.
Pfam PF09559: Cas6 Crispr (family)
The Cas6 Crispr family of proteins averaging 140 residues are characterised by having a GhGxxxxxGhG motif, where h indicates a hydrophobic residue, at the C-terminus. The CRISPR-Cas system is possibly a mechanism of defence against invading pathogens and plasmids that functions analogously to the RNA interference (RNAi) systems in eukaryotes.
Pfam PF12004: Disabled homolog 2-interacting protein, C-terminal domain (domain)
This domain is found at the C terminus of some GTPase-activating proteins (also known as GAP) found in animals, including Disabled homolog 2-interacting protein (DAB2P). This region is found associated with [pfam:PF00616] and [pfam:PF00168], and includes a coiled-coil domain that forms a parallel trimer in solution with one helical strand from each monomer.
Pfam PF12736: Cell-cycle sustaining, positive selection, (domain)
The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2.
Pfam PF20971: MASE12 (domain)
This is the membrane-associated sensor domain 12 (MASE12), found in (predicted) c-di-GMP phosphodiesterases and histidine kinases. This domain has conserved aromatic residues in the transmembrane segments, which suggests that its ligand could be a molecule with one or more aromatic rings.
Pfam PF01855: Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg (family)
This family includes the N terminal structural domain of the pyruvate ferredoxin oxidoreductase. This domain binds thiamine diphosphate, and along with domains II and IV, is involved in inter subunit contacts. The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited.
Pfam PF06427: UDP-glucose:Glycoprotein Glucosyltransferase (domain)
This domain consists of 7 stranded beta-sandwiches found in UDP-glucose-glycoprotein glucosyltransferase-like proteins. UDP-g_GGTase is an important, central component of the QC system in the ER for checking that glycoproteins are folded correctly. This QC prevents incorrectly folded glycoproteins from leaving the ER.
Pfam PF03701: Uncharacterised protein family (UPF0181) (family)
This family contains small proteins of about 50 amino acids of unknown function.                    The family includes YoaH [swissprot:P76260].
Pfam PF10319: Serpentine type 7TM GPCR chemoreceptor Srj (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srj is part of the Str superfamily of chemoreceptors. The srj family is designated as the out-group based on its location in preliminary phylogenetic analyses of the entire superfamily. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF03915: Actin interacting protein 3 (family)
This entry represents the C-terminal domain of actin interacting protein 3 (also known as Bud6 in budding yeasts). Bud6 is an actin- and formin-interacting protein. The N-terminal half of Bud6 is a microtubule binding domain required for its localisation and for its function in cortical capture of astral microtubule ends. The C-terminal half (residues 489-788) directly facilitates actin filament assembly by the formin Bni1 and is required for NPF (nucleation-promoting factor) activity. The domain represented in this entry (residues 365-776) is overlapped with the C-terminal half of Bud6 in this study . This entry also includes proteins from animals.
Pfam PF18967: Pycsar effector protein (family)
Pycsar (pyrimidine cyclase system for antiphage resistance) provides immunity against bacteriophage and consists of a pyrimidine cyclase (PycC), which synthesizes cyclic nucleotides in response to infection, and an effector protein. Cyclic nucleotides serve as specific second messenger signals, which activate the adjacent effector, leading to bacterial cell death and abortive phage infection. This family represents the effector protein from Pycsar system.
Pfam PF00646: F-box domain (domain)
This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; [pfam:PF00560] and [pfam:PF07723]) and the WD repeat ([pfam:PF00400]). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.
Wikipedia: F-box proteins are proteins containing at least one F-box domain. The first identified F-box protein is one of three components of the SCF complex, which mediates ubiquitination of proteins targeted for degradation by the 26S proteasome.
Pfam PF14144: Seed dormancy control (family)
This family of plant proteins appears to be a highly specific controller seed dormancy.
Pfam PF08203: Yeast RNA polymerase I subunit RPA14 (family)
This is a family of yeast proteins.  A14 is one of the final two subunits of Saccharomyces cerevisiae RNA polymerase I and is proposed to play a role in the recruitment of pol I to the promoter. Members of this entry has a HRDC domain, which is equivalent to that in subunit F from archaeal RNA polymerase II and RPB4 from the eukaryotic RNA polymerase II.
Pfam PF15037: Interleukin-17 receptor extracellular region (family)
This domain is found at the N-terminus (extracellular region) of interleukin-17 receptor C and Interleukin-17 receptor E. This is the presumed ligand-binding domain. Human putative interleukin-17 receptor E-like consists only of this domain.
Pfam PF13250: Domain of unknown function (DUF4041) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and viruses, and is approximately 60 amino acids in length. The family is found in association with [pfam:PF10544].
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 PF17997: Insecticidal delta-endotoxin CryIA(c) domain 5 (domain)
This domain is found in the protoxins portion of insecticidal proteins (parasporins, or Cry proteins) such as those from Bacillus thuringiensis (Bt) Cry1Ac. The protoxin portion comprise a proteolytically labile C-terminal segment (sometimes referred to as the protoxin domain). This is domain V in Cry1Ac from B. thuringiensis. One of the four protoxin domains (D-IV through D-VII). Domains V and VII are beta-rolls (similar to D-II or D-III) that closely resemble carbohydrate-binding modules (CBM) found in sugar hydrolases, however, it is difficult to guess which particular carbohydrates (if any) may serve as their ligands because residues on the putative sugar-binding interfaces are conserved neither in sequence nor in local structure. Structural analysis indicate that there are putative disulfide crosslinking at the dimer interface mediated by cysteines within 783-823 region of this domain which together with other cysteines creates a three-dimensional network of cross-links across the crystal which may play a role in stabilizing mature Bt Cry1Ac.
Pfam PF12926: Mitotic-spindle organizing gamma-tubulin ring associated (family)
FAM128A and FAM128B proteins have been re-named MOZART2A and B. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. The exact function of MOZART2 is not clear.
Pfam PF24657: Domain of unknown function (DUF7646) (domain)
This domain is found in uncharacterised proteins mainly from plants. It has detectable similarity to winged helix HTH domains and it is predicted to adopt similar structure.
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 PF06224: DNA glycosylase AlkZ-like (family)
This protein family includes DNA glycosylase AlkZ from Streptomyces sahachiroi (also known as Azi36) and similar proteins predominantly found in bacteria. AlkZ is an enzyme that provides self-resistance from azinomycin B (AZB) toxicity by unhooking interstrand cross- links (ICLs). The crystal structure of AlkZ revealed a C-shaped configuration with three tandem winged helix-turn-helix (wHTH) motifs and a positively charged surface that shows residues of great importance for the enzymatic activity.
Pfam PF05983: MED7 protein (family)
This family consists of several eukaryotic proteins which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus.
Wikipedia: Mediator of RNA polymerase II transcription subunit 7 is an enzyme that in humans is encoded by the MED7 gene.
Pfam PF05545: Cbb3-type cytochrome oxidase component FixQ (family)
This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon.
Pfam PF09242: Flavocytochrome c sulphide dehydrogenase, flavin-binding (domain)
Members of this family adopt a structure consisting of a beta(3,4)-alpha(3) core, and an alpha+beta sandwich. They are required for binding to flavin, and subsequent electron transfer.
Wikipedia: Flavocytochrome c sulfide dehydrogenase, also known as Sulfide-cytochrome-c reductase (flavocytochrome c) (EC 1.8.2.3), is an enzyme with systematic name hydrogen-sulfide:flavocytochrome c oxidoreductase. It is found in sulfur-oxidising bacteria such as the purple phototrophic bacteria Allochromatium vinosum. This enzyme catalyses the following chemical reaction:hydrogen sulfide + 2 ferricytochrome c  sulfur + 2 ferrocytochrome c + 2 H+
Pfam PF08150: FerB (NUC096) domain (domain)
This is central domain B in proteins of the Ferlin family.