SII-SWORD/CoKE huggingface dataset:
Pfam PF14711: Respiratory nitrate reductase beta C-terminal (domain)
This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between subunits and shielding of the Fe-S clusters
Pfam PF22523: Family of unknown function (DUF6999) (family)
This is a family of uncharacterised bacterial proteins. They are predicted to adopt alpha-helical structure. These proteins contain several invariant histidines and aspartates that may have a functional role.
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 PF24596: Family of unknown function (DUF7620) (coiled_coil)
This entry represents a family of small uncharacterised phage proteins that are predicted to form a coiled-coil. However, structure predictions do not predict homodimeric or homotrimeric complexes.
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 PF07527: Hairy Orange (domain)
The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split.  The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute.
Pfam PF06978: Ribonucleases P/MRP protein subunit POP1, N-terminal (domain)
This entry represents a conserved region approximately 150 residues long located towards the N-terminus of the POP1 subunit that is common to both the RNase MRP and RNase P ribonucleoproteins ([ec:3.1.26.5]). These RNA-containing enzymes generate mature tRNA molecules by cleaving their 5' ends. This is a short N-terminal domain consisting of a small helical core and a long alpha-helix, which is enriched with positively charged residues involved in pre-tRNA substrate recognition.
Pfam PF17943: Homeobox-cysteine loop-homeobox (domain)
This domain is considered a double homeodomain, termed HOCHOB, present in the C. elegans genome. Family members include CEH-91 and CEH-93 that share extended sequence similarity with each other upstream of their typical HDs (Homeodomains).  CEH-92, another family member, has three copies of this domain.  The domain consists of two divergent HDs that are separated by a linker of about 17 residues. The linker has a number of conserved positions, two of which are cysteine residues suggesting that they could be involved in metal binding. Hence, the name HOCHOB (Homeobox-cysteine loop-homeobox). Furthermore, there are two conserved histidine residues, one in each HD (in CEH-91 displaced by two positions), and there is also a conserved aspartic acid. It is speculated that the HOCHOB domain is an evolutionary novelty that is derived from two HDs and may have gained metal-binding capacity.
Pfam PF12361: Duffy-antigen binding protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 449 and 1061 amino acids in length. The family is found in association with [pfam:PF05424]. There are two conserved sequence motifs: NKNGG and QKHDF. This family is part of the Duffy-antigen binding protein of Plasmodium spp. This protein is an antigen on these parasites which enable them to invade erythrocytes.
Pfam PF03120: NAD-dependent DNA ligase OB-fold domain (domain)
DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small domain found after the adenylation domain [pfam:PF01653] in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding.
Pfam PF12239: Protein of unknown function (DUF3605) (family)
This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 161 and 256 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 PF02255: PTS system, Lactose/Cellobiose specific IIA subunit (domain)
The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a  variety of metabolic and transcriptional processes.  The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilised by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Pfam PF10719: Late competence development protein ComFB (family)
This family is conserved in bacteria. Some members, with three conserved cysteines, are annotated as late competence development protein ComFB.
Pfam PF11796: Protein of unknown function N-terminus (DUF3323) (family)
Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria).
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 PF16495: SWIRM-associated region 1 (family)
Much of the higher eukaryote SWI/SNF complex subunit SMARCC2 proteins is of low-complexity and or disordered. However, there are several short regions that are quite highly conserved. This is one of these regions.  The function of the individual regions is not known.
Pfam PF10762: Protein of unknown function (DUF2583) (family)
Some members in this family of proteins are annotated as YchH however currently no function is 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 PF22174: Tail protein, C-terminal domain (domain)
This domain is found at the C-terminal end of Tail protein, 43 kDa Neisseria meningitidis (NMB1110) and similar sequences found in tailed bacteriophages and prophages from proteobacteria. This domain is usually found associated with [pfam:PF21683].
Pfam PF20480: Family of unknown function (DUF6720) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in fungi. Proteins in this family are typically between 305 and 340 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 PF16362: YaiA protein (domain)
This family of proteins is found in Enterobacteriaceae, where they are immediately downstream of a Shikimate kinase.
Pfam PF14068: Putative membrane protein (family)
This family of bacterial proteins is functionally uncharacterised.  Proteins in this family are approximately 100 amino acids in length. There is a conserved FGIGF sequence motif, and many members are putative membrane proteins.
Pfam PF18092: DraK Histidine Kinase N-terminal domain (domain)
This is the N-terminal domain found in DraK Histidine Kinase (HK) present in Streptomyces coelicolor. Activation of the DraK HK leads to autophosphorylation of its kinase domain in the cytoplasm and subsequent transphosphorylation of DraR promoting blue-pigmented polyketide actinorhodin (ACT) production. The N-terminal domain is known as the sensor (or input) domain and undergoes a conformational change resulting in phosphorylation of a conserved histidine in its cytoplasmic kinase domain.
Pfam PF13855: Leucine rich repeat (repeat)
Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape . LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions .Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response .

Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel Î² sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the Î²-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with Î±-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions . Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20-to 30-residue repeats .
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF02392: Ycf4 (family)
This family consists of hypothetical Ycf4 proteins from various chloroplast genomes.  It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts.
Pfam PF15294: Leucine zipper (family)
This family includes Leucine zipper transcription factor-like protein 1 (LZTFL1) and Leucine zipper protein 2 (LUZP2).
Pfam PF09209: HTH-type transcriptional dual regulator CecR, C-terminal domain (domain)
This entry represents the C-terminal domain found in CecR (regulator  of cefoperazone and chloramphenicol sensitivity), previously known  as YbiH. CecR has been shown to control sensitivity to cefoperazone  and chloramphenicol through regulating the transcription of the  cecR-ybhGFSR operon and the rhlE gene.
Pfam PF18387: Zinc-fingers and homeoboxes C2H2 finger domain (domain)
This is a C2H2 zinc-finger domain found in ZHX proteins such as ZHX1. ZHXs are multidomain proteins comprising two C2H2 zinc finger motifs and five homeodomains. Both homeodomains and zinc fingers are short protein modules involved in protein-DNA and/or protein-protein interactions; they are frequently associated with roles in transcriptional regulation. All members of the ZHX family are reported to be able to form both homo- and heterodimers via the region containing homeodomain 1. ZHX1 is a transcriptional repressor which is ubiquitously expressed. It interacts with nuclear factor Y subunit A (NFYA) and DNA methyl transferase 3B (DNMT3B) for its repression activity. Changes in expression profiles of rat ZHX1 ortholog have been associated with glomerular disease. In addition to the five homeodomains, ZHX1, which also contains of two N terminal C2H2 zincfingers forms homodimers via homeodomain and can also form heterodimers with ZHX3.
Pfam PF18885: Domain of unknown function (DUF5648) (domain)
This entry represents a three-bladed beta-alpha propeller domain with unknown function.  It is often associated with enzymatic domains in bacterial cell surface proteins.  Individual blade consist of a three-stranded antiparallel beta-sheet and an alpha-helix packed on it. In some members this helix may have transitioned to a random coil.
Pfam PF20251: Bacterial Ig-like domain (domain)
This bacterial Ig-like domain shows some similarity to [pfam:PF12690] suggesting it may act as a protease inhibitor similar to B. subtilis BsuPI.
Pfam PF13625: Helicase conserved C-terminal domain (domain)
This domain family is found in a wide variety of helicases and helicase-related proteins.
Pfam PF07821: Alpha-amylase C-terminal beta-sheet domain (domain)
This domain is organised as a five-stranded  anti-parallel beta-sheet. It is the  probable result of a decay of the common-fold.
Wikipedia: α-Amylase is an enzyme that hydrolyses α bonds of large, α-linked polysaccharides, such as starch and glycogen, yielding shorter chains thereof, dextrins, and maltose, through the following biochemical process:Endohydrolysis of (1→4)-α-D-glucosidic linkages in polysaccharides containing three or more (1→4)-α-linked D-glucose units
Pfam PF12164: Stage V sporulation protein AA (domain)
This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up.
Pfam PF01235: Sodium:alanine symporter family (family)
Sodium symporters can be divided by sequence and functional similarity into various groups. One such group is the sodium/alanine symporter family, the members of which transport alanine in association with sodium ions.

These transporters have between 10-14 transmembrane (TM) helices , characterised by a five or seven transmembrane helix inverted-topology repeat motif, forming a channel or pore through the cytoplasmic membrane, the interior face being hydrophilic to allow the passage of alanine molecules and sodium ions . This family is restricted to the bacteria and archaea, examples are the alanine carrier protein from the Bacillus PS3 (Thermophilic bacterium PS-3); the sodium/alanine symporter AgcS from Methanococcus maripaludis , the D-alanine/glycine permease from Pseudoalteromonas haloplanktis (Alteromonas haloplanktis); and the hypothetical protein yaaJ from Escherichia coli.
Wikipedia: Members of the Alanine or Glycine:Cation Symporter (AGCS) Family (TC# 2.A.25) transport alanine and/or glycine in symport with Na+ and or H+.
Pfam PF19931: Family of unknown function (DUF6394) (family)
This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are typically between 113 and 127 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 PF08013: D-tagatose-1,6-bisphosphate aldolase subunit GatZ/KbaZ-like (domain)
Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also  called agaY, agaZ). The catalytic subunits GatY/KbaY alone are  sufficient to show aldolase activity and contain most or all of the  residues that have been identified as essential in substrate/product  recognition and catalysis for class II aldolases. However,  these aldolases differ from other Class II aldolases (which are  homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits  alone do not show any aldolase activity. This entry represents GatZ and KbaZ subunits. This entry also includes the D-tagatose  6-phosphate 4-epimerase Atu3167 from Agrobacterium fabrum which catalyzes the epimerization of D-tagatose 6-phosphate to D-fructose 6-phosphate. It should be noted that the previous suggestion of  a tagatose 6P-kinase function for other members of this family has   been debated.
Pfam PF15617: C-C_Bond_Lyase of the TIM-Barrel fold (family)
This family of TIM-Barrel fold C-C bond lyase is related to citrate-lyase. These genes are found in the biosynthetic operon, with other enzymatic domains, associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response.
Pfam PF01886: Protein of unknown function DUF61 (family)
This Domain of unknown function 61 (DUF61) family of proteins are widely distributed in archaea. In crenarchaea, the genes of DUF61 proteins are in an operon containing two genes of box C/D RNA protein complexes. The NMR structure of a DUF61 family member from the hyperthermophilic archaeon Sulfolobus solfataricus revealed a rigid core structure and flexible N- and C-terminal regions, including a negatively-charged independent C-terminal helix. The core structure consists of N- and C-terminal subdomains, in which the C-terminal subdomain shows significant structural similarity with several nucleic acid binding 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 PF18321: 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain (domain)
This domain is found in 3-hydroxybutyryl-CoA dehydrogenase present in E. coli. 3-hydroxybutyryl-CoA dehydrogenase catalyzes the second step in the biosynthesis of n-butanol from acetyl-CoA, in which acetoacetyl-CoA is reduced to 3-hydroxybutyryl-CoA. This domain is a reduced Rossmann-fold domain and, unlike the first Rossmann-fold domain, it is missing the catalytic residues and an NAD(H) binding cleft.
Pfam PF07497: Rho termination factor, RNA-binding domain (domain)
The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts.  It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers.
Pfam PF01134: Glucose inhibited division protein A (family)
MnmG (also known as GidA) is a tRNA modification enzyme found in bacteria and mitochondria. MnmG forms a complex with MnmE which is involved in the formation of methyluridine derivatives at the wobble uridine base in some tRNAs .

This domain is also found in the MnmG paralogue TrmFo, a folate/FAD-dependent methyltransferase that catalyzes the methylation of the C5-uridine 54 in the T-loop of tRNAs of most Gram-positive bacteria and some Gram-negative bacteria . TrmFO lacks a C-terminal helical domain present in MnmG .

This entry represents the N-terminal domain of MnmG and related domains. This domain does not include the C-terminal region of MnmG, which contains a sterile alpha motif domain and is responsible for tRNA-protein and protein-protein interactions including association with MnmE .
Pfam PF02514: CobN/Magnesium Chelatase (family)
This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis.
Wikipedia: Magnesium-chelatase is a three-component enzyme (EC 6.6.1.1) that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of chlorophyll and bacteriochlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth:
Pfam PF22961: Reversion-inducing cysteine-rich with Kazal motifs, N-terminal (domain)
This domain is found repeated at the N-terminal end of human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar proteins mainly predominantly found in vertebrates. RECK is a membrane-anchored glycoprotein that plays a role in Wnt7-specific responses in the central nervous system angiogenesis and in the blood-brain barrier regulation. This domain adopts an alpha-helical configuration.
Pfam PF01295: Adenylate cyclase, class-I (family)
Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases . Class I cyclases are found in enterobacteria and related Gram-negative bacteria.
Wikipedia: Adenylate cyclase is an enzyme with systematic name ATP diphosphate-lyase . It catalyzes the following reaction:ATP = 3′,5′-cyclic AMP + diphosphate