SII-SWORD/CoKE huggingface dataset:
Pfam PF24533: Ada2b-like, C-terminal tri-helical domain (domain)
This domain is found at the C-terminal end of Transcriptional adapter 2B from Drosophila melanogaster (Ada2b) and similar animal proteins. Ada2b is required for the function of some acidic activation domains, which activate transcription from a distant site. This domain is predicted to show a tri-helical structure.
Pfam PF05097: Protein of unknown function (DUF688) (family)
This family contains several uncharacterised proteins found in Arabidopsis thaliana.
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 PF03912: Psb28 protein (family)
Psb28 is a 13 kDa soluble protein that is directly assembled in dimeric PSII supercomplexes.  The negatively charged N-terminal region is essential for this process. This protein was formerly known as PsbW, but PsbW is now reserved for [pfam:PF07123].
Pfam PF02579: Dinitrogenase iron-molybdenum cofactor (family)
This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyses the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.
Pfam PF14293: YWFCY protein (family)
This entry is found in bacteria, and is approximately 140 amino acids in length. It represents an integral membrane region found in many Type IV secretion protein. There is a conserved YWFCY motif. It is often found in association with [pfam:PF02534].
Pfam PF10363: Required for nuclear transport of RNA pol II C-terminus 1 (repeat)
This domain is found towards the C-terminus of required for the nuclear transport of RNA pol II protein (RTP1). RTP1 is required for the nuclear localisation of RNA polymerase II. This family is found in association with [pfam:PF10304].
Pfam PF20647: Domain of unknown function (DUF6808) (domain)
This is a domain of unknown function that is found in archaea and bacteria. This domain is typically around 110 amino acids in length. There are two conserved motifs, RW and VSG.
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 PF02293: AmiS/UreI family transporter (family)
This family includes UreI and proton gated urea channel as well as putative amide transporters.
Wikipedia: The proton-gated urea channel is an inner-membrane protein essential for the survival to Helicobacter pylori. It enables the rapid influx of urea into the bacterium. It is closed at pH 7.0 and fully open at pH 5.0. Urease activity buffers the periplasm to pH 6.1. Using multiwavelength anomalous dispersion (MAD), its structure, a compact hexameric ring about 95 Å in diameter and 45 A ̊ in height, was determined. The centre is filled with a lipid plug that forms an asymmetric bilayer. Amino residues that can be protonated in the periplasmic domain are important for proton sensing or gating.
Pfam PF19060: DVNP family (family)
Dinoflagellate viral nucleoprotein (DVNPs) are known to function in DNA packaging in Dinoflagellate as a histone replacement. It displaces nucleosomes when expressed in yeast. This family is predominantly found in Phycodnaviridae.
Pfam PF15977: Winged helix-turn-helix DNA binding (family)
This winged helix-turn-helix DNA-binding domain is found in IprA, a protein involved in oxidative stress resistance in Proteobacteria .
Pfam PF01596: O-methyltransferase (domain)
Members of this family are O-methyltransferases. The family includes catechol o-methyltransferase [swissprot:P21964], caffeoyl-CoA O-methyltransferase [swissprot:Q43095] and a family of bacterial O-methyltransferases that may be involved in antibiotic production.
Pfam PF21246: Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain (repeat)
This domain is found at the N-terminal end of Ubiquitin carboxyl- terminal hydrolase 38 from humans and similar proteins found in vertebrates. This domain forms ARM repeats. It is often associated to [pfam:PF00443].
Pfam PF21284: Complement component C7, FIM2 N-terminal (domain)
Factor I-like modules (FIMs) are present in complement proteins C6, C7, and factor I, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. Complement component C7 contains a FIM pair at the C-terminal, FIM1 and FIM2; each of them consists of a small N-terminal FOLN subdomain and a larger C-terminal KAZAL domain ([pfam:PF18434]). This entry represents the N-terminal of FIM2; it has a FOLN architecture which is a truncated form of the epidermal growth factor domain (EGF).
Pfam PF11760: Cobalamin synthesis G N-terminal (domain)
Members of this family are involved in cobalamin synthesis.  The gene encoded by [swissprot:P72862] has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process. Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B. The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF22480: Domain of unknown function (DUF6984) (domain)
This entry represents a bacterial family 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 PF19900: Family of unknown function (DUF6373) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001517) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the asperphenamate biosynthetic gene cluster from Aspergillus terreus NIH2624.
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 PF05880: Fijivirus 64 kDa capsid protein (family)
This family consists of several Fijivirus 64 kDa capsid proteins.
Pfam PF09092: Lyase, N terminal (domain)
Members of this family are predominantly found in chondroitin ABC lyase I, and adopt a jelly-roll fold topology consisting of a two-layered bent beta-sheet sandwich with one short alpha-helix. The convex beta sheet is composed of five antiparallel strands, whilst the concave beta-sheet contains five antiparallel beta-strands with a loop between two consecutive strands folding back onto the concave surface. This domain is required for binding of the protein to long glycosaminoglycan chains.
Pfam PF17284: Spermidine synthase tetramerisation domain (domain)
This domain represents the N-terminal tetramerization domain from spermidine synthase.
Pfam PF20007: FtsH ternary system-associated peptide (family)
Predicted peptide-effector encoded as standalone domain in some FtsH ternary system neighborhoods. Likely modified by the Radical SAM domain also found in these neighborhoods. The FtsH ternary systems are a class of NTP-dependent biological conflict systems.
Pfam PF13638: PIN domain (domain)
Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).
Wikipedia: In molecular biology the PIN domain is a protein domain that is about 130 amino acids in length. PIN domains function as nuclease enzymes that cleave single stranded RNA in a sequence- or structure-dependent manner.
Pfam PF01868: Ribonuclease P/MRP, subunit p29 (family)
This family consists of several archaeal and eukaryotic proteins. The archaeal proteins are found to be expressed within ribosomal operons and several of the sequences are described as ribonuclease P protein subunit p29 proteins. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex. Rpp29 catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits.
Pfam PF02771: Acyl-CoA dehydrogenase, N-terminal domain (domain)
The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain.
Pfam PF04864: Allinase (domain)
Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulfoxide cysteine derivatives by alliinase ([ec:4.4.1.4]), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system.
Wikipedia: In enzymology, an alliin lyase is an enzyme that catalyzes the chemical reactionan S-alkyl-L-cysteine S-oxide  an alkyl sulfenate + 2-aminoacrylate
Pfam PF12985: Domain of unknown function (DUF3869) (domain)
A family based on the N-terminal domain of 3KOG, which shows weak but consistent remote homology with adhesive families such as immunoglobulins and cadherins, suggesting it might form an attachment module.
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 PF04914: DltD protein (family)
DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid.  This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine.  DltD does not ligate acyl carrier protein (ACP) with D-alanine.   It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis.
Pfam PF11263: Borrelia burgdorferi attachment protein P66 (family)
P66 is an outer membrane protein in Borrelia burgdorferi, the agent of Lyme disease. P66 has a role in the attachment of Borrelia burgdorferi to human cell-surface receptors.
Pfam PF20865: FAM186A/B, C-terminal (domain)
This is the C-terminal helical domain found in FAM186A/B and similar proteins. The function of FAM186A/B is not known.
Pfam PF21653: Pullulanase, all-beta domain (domain)
This entry represents the all-beta domain found at the C-terminal of pullulanase A proteins, members of the glycosyl hydrolase family 13.
Pfam PF11042: Protein of unknown function (DUF2750) (family)
This family is conserved in Proteobacteria. The function is not known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13686: DsrE/DsrF/DrsH-like family (family)
DsrE is a small soluble protein involved in intracellular sulfur reduction. The family also includes YrkE proteins.
Pfam PF07030: Bacteriophage Mu, Gp36 (family)
This family is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Pfam PF03299: Transcription factor AP-2 (family)
Activator protein-2 (AP-2) transcription factors constitute a family of closely related and evolutionarily conserved proteins that bind to the DNA consensus sequence 5'-GCCNNNGGC-3' and stimulate target gene transcription . Five different isoforms of AP-2 have been identified in mammals, termed AP-2 alpha, beta, gamma, delta and epsilon. Each family member shares a common structure, possessing a proline/glutamine-rich domain in the N-terminal region, which is responsible for transcriptional activation , and a helix-span-helix domain in the C-terminal region, which mediates dimerisation and site-specific DNA binding .

The AP-2 family have been shown to be critical regulators of gene expression during embryogenesis. They regulate the development of facial prominence and limb buds, and are essential for cranial closure and development of the lens ; they have also been implicated in tumorigenesis. AP-2 protein expression levels have been found to affect cell transformation, tumour growth and metastasis, and may predict survival in some types of cancer . Mutations in human AP-2 have been linked with bronchio-occular-facial syndrome and Char Syndrome, congenital birth defects characterised by craniofacial deformities and patent ductus arteriosus, respectively .
This entry represents the C-terminal region of these proteins, including the helix-span-helix domain.
Pfam PF00859: CTF/NF-I family transcription modulation region (family)
Nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF)  (also known as TGGCA-binding proteins) are a family of vertebrate nuclear proteins which recognise and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. This family was first described for its role in stimulating the initiation of adenovirus DNA replication . In vertebrates there are four members NFIA, NFIB, NFIC, and NFIX and an orthologue from Caenorhabditis elegans has been described, called Nuclear factor I family protein (NFI-I) . The CTF/NF-I proteins are individually capable of activating transcription and DNA replication, thus they function by regulating cell proliferation and differentiation. They are involved in normal development and have been associated with developmental abnormalities and cancer in humans . In a given species, there are a large number of different CTF/NF-I proteins, generated both by alternative splicing and by the occurrence of four different genes. CTF/NF-1 proteins contain 400 to 600 amino acids. The N-terminal 200 amino-acid sequence, almost perfectly conserved in all species and genes sequenced, mediates site-specific DNA recognition, protein dimerisation and Adenovirus DNA replication. The C-terminal 100 amino acids contain the transcriptional activation domain. This activation domain is the target of gene expression regulatory pathways elicited by growth factors and it interacts with basal transcription factors and with histone H3 .
Pfam PF15951: MITF/TFEB/TFEC/TFE3 N-terminus (family)
This domain is found at the N-terminus of several transcription factors including microphthalmia-associated transcription factor, transcription factor EB, transcription factor EC and transcription factor E3.
Pfam PF22692: Flagellar hook protein FlgE/F/G D1 domain (domain)
This entry represents the D1 domain found in three closely related flagellar proteins usually denoted FlgE, FlgF and FlgG. In FlgE there is an additional domain (D2, [pfam:PF07559]) outside D1. The flagellar hook is a short, highly curved tubular structure that connects the flagellar motor to the long filament acting as a helical propeller.
Pfam PF17064: Quiver family u-PAR/Ly-6-like domain (domain)
In Drosophila QUIVER (also known as SLEEPLESS protein or SSS) is a (GPI)-anchored protein required for homoeostatic regulation of sleep under normal conditions and following sleep deprivation. It is a novel potassium channel subunit that modulates the Shaker (Sh) potassium channel which regulates the sleep. Besides the Sh modulation, SSS also antagonises nicotinic acetylcholine receptors (nAChRs) to reduce synaptic transmission and promote sleep.
Pfam PF01978: Sugar-specific transcriptional regulator TrmB (domain)
One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Pfam PF19999: FtsH ternary system domain X3 (domain)
Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF08879: WRC (domain)
The WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localisation  signal and a zinc-finger motif (C3H). It is suggested that  the WRC domain functions in DNA binding.
Pfam PF15206: FAM209 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between and 170 amino acids in length. Although the exact function of this family is unknown, it has been suggested that it may play a role in sperm acrosome biogenesis.
Pfam PF11998: Low psii accumulation1 / Rep27 (family)
This family includes members such as low psii accumulation1 (lpa1) from plants as well as Rep27 proteins found in unicellular green alga Chlamydomonas reinhardtii. The Arabidopsis LPA1 is a chaperone required for efficient photosystem II (PSII) assembly. It binds to psbA during de novo biogenesis of PSII. Other studies show that REP27 in Chlamydomonas reinhardtii chloroplast thylakoids, plays a dual role in the regulation of D1 protein turnover by facilitating cotranslational biosynthesis insertion (C-terminal domain) and activation (tetratricopeptide repeat [TPR] motifs) of the nascent D1 during the PSII repair process.
Pfam PF21503: Centriolar protein SAS, helical domain (domain)
This domain is found in Spindle assembly abnormal protein 6 from Caenorhabditis elegans (Sas-6), which is essential for centriole formation. This domain is C-terminal to [pfam:PF16531]. It shows an alpha-helical conformation.
Pfam PF11238: Protein of unknown function (DUF3039) (family)
This family of proteins with unknown function appears to be restricted to Actinobacteria.
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 PF06221: Putative zinc finger motif, C2HC5-type (domain)
This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4.
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF06412: Conjugal transfer protein TraD (family)
This family contains bacterial TraD conjugal transfer proteins.  Mutations in the TraD gene result in loss of transfer.
Pfam PF14201: Domain of unknown function (DUF4318) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There is a single completely conserved residue F that may be functionally important.
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 PF16960: Haemoglobin-haptoglobin utilisation, porphyrin transporter (family)
HpuA is a family of Neisseria spp proteins from the hpuAB operon, which are putative porphyrin transporters.
Pfam PF08099: Scorpion calcine family (family)
This family consists of the calcine family of scorpion  toxins. The calcine family consists of Maurocalcine and  Imperatoxin. These toxins have been shown to be potent  effector of ryanodyne-sensitive calcium channel from  skeletal muscles. These toxins are thus useful for  dihydropyridine receptor/ryanodyne receptor interaction  studies.
Pfam PF09300: Tectiviridae, minor capsid (domain)
Members of this family form the minor capsid protein of various Tectiviridae.
Pfam PF12852: Cupin (domain)
This is a family of bacterial and eukaryotic proteins that belong to the Cupin superfamily.  Some of the proteins in this family are annotated as being members of the AraC family of transcription factors, in which case this domain corresponds to the ligand binding domain.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.