SII-SWORD/CoKE huggingface dataset:
Pfam PF07777: G-box binding protein MFMR (family)
This region is found to the N-terminus of the [pfam:PF00170] transcription factor domain.  It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to  motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals.
Pfam PF17566: Family of unknown function (DUF5472) (family)
This is a family of unknown function found in Human papillomavirus.
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 PF10333: GPI-Mannosyltransferase II co-activator (family)
Pga1 is found only in yeasts and not in mammals. It localises in the ER as a glycosylated integral membrane protein. It binds to the GPI-mannosyltransferase II subunit of the GPI and it is responsible for the second mannose addition to GPI precursors. The GPI-anchoring complex is a glycolipid that functions as a membrane anchor for many cell-surface proteins.
Pfam PF08679: Dissimilatory sulfite reductase D (DsrD) (family)
The structure of the DsrD protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins.  The structure suggests a possible role for DsrD in transcription of translation of genes which catalyse dissimilatory sulfite reduction.
Pfam PF19409: Thiopeptide-type bacteriocin precursor (family)
This entry represents a member of a biosynthetic gene cluster (BGC). The BGC (BGC0001753) is described by MIBiG as an example of a RiPP (ribosomally synthesised and post-translationally modified  peptide) BGC. Members of this protein family are the precursors of  a family of small bacteriocins (i.e. microcins) with thiopeptide  type modifications, a highly modified subclass of heterocycle- containing peptide antibiotics.
Pfam PF15760: Leukemia-associated protein 7 (family)
Leukemia-associated protein 7 (DLEU7 or LEU7) is a gene of unknown function deleted in lymphocytic leukemia . It is a vertebrate-specific gene that might have a role in development .
Pfam PF10390: RNA polymerase II elongation factor ELL (family)
ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF. Some members carry an Occludin domain [pfam:PF07303] just downstream. There is no S. cerevisiae member.
Pfam PF20048: Domain of unknown function (DUF6450) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in phages, and is approximately 60 amino acids in length. It contains the conserved sequences WSxxxLTxY and DPTFIASVFTG.
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 PF14531: Kinase-like (family)
This family includes the pseudokinases ROP2 and ROP8 from Toxoplasma gondii ([swissprot:Q06AK3] and [swissprot:O15693]). These proteins have a typical bilobed protein kinase fold, but lack catalytic actvity.
Pfam PF04467: Protein of unknown function (DUF483) (family)
Family of uncharacterised prokaryotic 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 PF04573: Signal peptidase subunit (family)
Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC) which consists of four subunits in yeast and five in mammals.  This family is common to yeast and mammals.
Wikipedia: Signal peptidases are enzymes that convert secretory and some membrane proteins to their mature or pro forms by cleaving their signal peptides from their N-termini.
Pfam PF14886: FAM183A and FAM183B related (family)
This family includes Cilia- and flagella-associated protein 144 (CFAP144, also known as FAM183A) from human and its homologues. This is a microtubule inner protein (MIP) part of the dynein- decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.
Pfam PF22442: Gp49, pectin lyase-like (repeat)
This entry represents the beta-helix repeats from the catalytic domain of tailspike Gp49 from phage LKA1. Gp49 binds and cleaves B-band LPS of Pseudomonas aeruginosa, reducing its virulence.
Pfam PF12615: F sex factor protein N terminal (family)
This domain family is found in bacteria, and is typically between 96 and 107 amino acids in length. The family is found in association with [pfam:PF10412]. TraD is a cytoplasmic membrane protein with possible DNA binding domains. It is part of the bacterial F sex factor complex.
Pfam PF10422: Monopolin complex subunit LRS4 (family)
Monopolin is a protein complex, originally identified in Saccharomyces cerevisiae, that is required for the segregation of homologous centromeres to opposite poles of a dividing cell during meiosis I. The orthologous complex in Schizosaccharomyces pombe is not required for meiosis I chromosome segregation, but is proposed to play a similar physiological role in clamping microtubule binding sites. In S .cerevisiae this subunit is called LRS4, and in S. pombe it is known as Mde4.
Pfam PF13756: Stimulus-sensing domain (family)
This domain is found in the periplasmic region of the sensor component of the two-component regulatory system. The periplasmic region is likely to be involved in stimulus sensing.
Pfam PF24727: Domain of unknown function (DUF7679) (domain)
This entry represents a small family of Lactobacillus proteins of unknown function. The predicted structure suggests these proteins contain two subdomains, with an N-terminal partly open beta barrel and C-terminal alpha/beta subdomain.
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 PF04751: Dual-action ribosomal maturation protein DarP (family)
The entry, previously known as DUF615, represents the Dual-action ribosomal maturation protein DarP (also known as YjgA) from Escherichia coli and related proteins. This protein binds pre-50S ribosomal subunits near the 23S rRNA L1 stalk, where it probably mediate correct positioning of the L1 stalk. It plays a dual role in the late stages of assembly of the 50S ribosomal subunit where it promotes peptidyl transferase center maturation by modulating the docking of 23S rRNA helix H68, and maintains the stability of helix H89 with the help of uL16 (rplP), facilitating the final maturation of the peptidyl transferase center.
Pfam PF15978: Tn7-like transposition protein D (family)
TnsD is a family of putative Tn7-like transposition proteins type D.
Pfam PF01796: ChsH2, C-terminal OB-fold domain (domain)
This domain is found at the C-terminal end of the probable enoyl -CoA hydratase alpha subunit from Thermomonospora curvata (ChsH2) and similar archaeal and bacterial proteins. ChsH2 is likely to be involved in bile acid degradation. The C-terminal region of this protein is organised into two domains: an N-terminal zinc finger domain ([pfam:PF12172]) and an OB-fold domain (this entry) that consists of a five-stranded beta-barrel. This domain is also found in 3-oxo-4,17- pregnadiene-20-carboxyl-CoA hydratase alpha subunit from Mycobacterium tuberculosis that is involved in cholesterol side chain degradation. It is also found in Methanothermococcus thermolithotrophicus HMGCS, an enzyme complex comprising the thiolase and 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase, that catalyses the second reaction in the mevalonate pathway-the exergonic condensation of acetoacetyl-CoA and acetyl-CoA to HMG-CoA.
Pfam PF03439: Early transcription elongation factor of RNA pol II, NGN section (family)
Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4.  Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.
Pfam PF19045: Ligase-CoA domain (domain)
This domain is related to [pfam:PF00549] and adopts a flavodoxin fold.
Pfam PF22628: ZAP-like CCCH zinc finger (domain)
This domain is found in Zinc finger CCCH-type antiviral protein 1 from Rattus norvegicus (Zc3hav1, also known as ZAP), which inhibits the replication of viruses by recruiting the cellular RNA degradation machineries to degrade the viral mRNAs. This protein has four zinc-finger motifs that are located at the four corners of a twisted rectangle in the bottom layer of the structure.
Pfam PF04084: Origin recognition complex subunit 2 RecA-like domain (domain)
All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. This entry represents the RecA-like domain of ORC2 with no predicted ATPase activity.
Wikipedia: Origin recognition complex subunit 2 is a protein that is encoded by the ORC2 (ORC2L) gene in humans.
Pfam PF18391: CHIP N-terminal tetratricopeptide repeat domain (repeat)
This is N-terminal tetratricopeptide repeat (TPR) domain found in C terminus of Hsp70 interacting proteins (CHIP). The TPR domain of CHIP binds directly to EEVD motifs located at the C termini of Hsc/Hsp70 and Hsp90.
Pfam PF17086: Small capsid protein of Herpesviridae (family)
This is a family of herpes-type viral small capsid proteins.
Pfam PF20911: Major capsid protein GP7 (family)
This family represents Major capsid protein GP7 from Salmonella phage epsilon15 and similar proteins found in tailed bacteriophages and bacterial prophages. GP7 adopts a canonical phage structure, showing different structural features (an N-arm, an F-loop, an E-loop, a P-domain, a long alpha-helix, an A-domain and the C-terminal end).
Pfam PF24879: Domain of unknown function (DUF7737) (domain)
This domain is found in proteins that contain [pfam:PF13569]. The function of this domain is 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 PF16967: E-set like domain (domain)
TcfC is a family of bacterial fimbrial proteins. These sit in the outer bacterial membrane surrounding the RcpA proteins of the fimbrial shaft. This family is from Gamma-proteobacteria. This domain represents an immunoglobulin like E-set domain.
Pfam PF15601: Immunity protein 70 (family)
A predicted immunity protein with an alpha+beta fold and conserved tyrosine and tryptophan residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-REase-10 family.
Pfam PF04955: HupE / UreJ protein (family)
This family of proteins are hydrogenase / urease accessory proteins.  The alignment contains many conserved histidines that are likely to be involved in nickel binding. The members usually have five membrane-spanning regions.
Pfam PF20587: Family of unknown function (DUF6789) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. These are likely  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 PF21542: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is found at the C-terminal end of a group of prokaryotic transcriptional regulators, including AcrR1 from Aquifex aeolicus. It shows an all-alpha structure.
Pfam PF17015: Domain of unknown function (DUF5094) (family)
This family of largely microsporidial-specific proteins is of unknown function.  However there may be distant homology to family Csm1, [pfam:PF12539].
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 PF20159: YidB-like protein (family)
This entry includes the uncharacterised protein YidB from E. coli [swissprot:P09996]. This entry was previously a subset of the DUF937 family.
Pfam PF04359: Protein of unknown function (DUF493) (domain)
This domain is likely to act in a regulatory capacity like [pfam:PF01842] domains. This domain has a remarkable property in that the C-terminal residue of every protein in the family lies up in the alignment. This suggests that the C-terminal residue plays some important functional role (Bateman A pers obs).
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 PF08774: VRR-NUC domain (domain)
This is the VRR-NUC domain, a member of the PD-(D/E)XK nuclease superfamily found in FAN1 and type III restriction modification enzymes. FAN1 is a a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks. FAN1 is the only eukaryotic protein with a VRR-NUC domain. This domain is also found in TseVs antibacterial effectors secreted by the type VI secretion system (T6SS). TseVs are evolutionary related to Holliday junction resolvases and enzymes involved in DNA interstrand crosslink repair.
Pfam PF06681: Protein of unknown function (DUF1182) (family)
This family consists of several hypothetical proteins of around 360 residues in length and seems to be specific to Caenorhabditis elegans. The function of this family is unknown. It appears to carry seven TM regions.
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 PF20558: Family of unknown function (DUF6769) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically 136 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 PF03355: Viral Trans-Activator Protein (family)
These proteins function as a trans-activator of viral late genes.
Pfam PF19476: Family of unknown function (DUF6013) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001120) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the burkholderic  acid biosynthetic gene cluster from Burkholderia thailandensis E264  and appears to be predominantly found in Burkholderiaceae
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 PF08302: Fungal tRNA ligase phosphodiesterase domain (domain)
This domain is found in fungal tRNA ligases and has cyclic phosphodiesterase activity.  tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.
Pfam PF04180: Low temperature viability protein (family)
The low-temperature viability protein LTV1 is involved in ribosome  biogenesis 40S subunit production.
Pfam PF17601: Family of unknown function (DUF5497) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF02090: Salmonella surface presentation of antigen gene type M protein (coiled_coil)
The Salmonella typhimurium Surface Presentation of Antigens M gene (SpaM) is one of 12 that form a cluster responsible for invasion properties . The gene product is required for entry by the bacterium into epithelial cells, and is thus considered to be a virulence factor . Other Spa genes in the cluster are related to invasion (Inv) genes in similar Salmonella and Shigella species , and flagella biosynthesis genes in Helicobacter pylori .

A homologue of this protein has been found recently in Salmonella enterica . The protein, named InvI, is required by the organism to gain access to mammalian epithelial cells, and cellular mutants (InvI-) failed to successfully infect these cells. It has also been found that the inv-spa loci of this particular species encode for a type III protein secretion system, essential in the bacterium's host cell invasion process .
Pfam PF06748: Protein of unknown function (DUF1217) (family)
This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies.
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 PF03636: Glycosyl hydrolase family 65, N-terminal domain (family)
This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose.  This domain is believed to be essential for catalytic activity although its precise function remains unknown.
Wikipedia: In molecular biology, glycoside hydrolase family 65 is a family of glycoside hydrolases.
Pfam PF03799: Cell division protein FtsQ/DivIB, C-terminal (domain)
FtsQ is an essential cell division protein. It may link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. FtsQ may control the correct divisome assembly. DivIB is a cell division protein from Gram-positive bacteria, probably homologous to Escherichia coli FtsQ. DivIB interacts with FtsL, DivIC and PBP-2B. DivIB plays an essential role in division at high temperatures, maybe by protecting FtsL from degradation or by promoting formation of the FtsL-DivIC complex. It is also required for efficient sporulation at all temperatures. FtsQ and DivIB have a short N-terminal cytoplasmic domain and a larger C-terminal periplasmic domain. This entry represents the C-terminal region.
Pfam PF01826: Trypsin Inhibitor like cysteine rich domain (domain)
This family contains trypsin inhibitors as well as a domain found in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9.
Pfam PF23660: NOMO eighth prealbumin-like domain (domain)
This domain is found in the NOMO family of proteins such as NOMO1, NOMO2, NOMO3. These proteins are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. NOMO proteins are multidomain proteins. This entry represents the eight domain that is predicted to fold into a beta-sandwich with prealbumin-like topology.