SII-SWORD/CoKE huggingface dataset:
Pfam PF23332: RECK-like, CC4 domain (domain)
This domain is found in Reversion-inducing cysteine-rich protein with Kazal motifs from Mus musculus (RECK) and similar proteins from animals. RECK play essential roles in signalling in the central nervous system vascular development, acting to enable brain endothelial cells to selectively respond to Wnt7 signals (WNT7A or WNT7B). This protein contains five tandem and highly divergent repeats with six cysteines each and characteristic spacing. These units are named 'CC domains'. This entry represents the fourth of these domains (CC4), which consists of four short alpha-helices stabilised by three disulfide bonds.
Pfam PF17389: Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain (repeat)
This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria.
Wikipedia: In molecular biology, glycoside hydrolase family 78 is a family of glycoside hydrolases.
Pfam PF03342: Rhabdovirus M1 matrix protein (M1 polymerase-associated protein) (family)
This is a family of phosphoproteins of unknown function expressed by Rhadovirus.
Pfam PF04435: Domain of unknown function (DUF545) (family)
Family of uncharacterised C. elegans proteins. The region represented by this family can is found to be repeated up to four time in some proteins.
Pfam PF08895: Domain of unknown function (DUF1840) (domain)
This family of proteins are functionally uncharacterised.
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 PF10357: KIN17 WH-like domain (domain)
This entry represents the WH-like domain found in the central region of KIN17 proteins, which folds into an atypical winged helix (WH) domain. It consists of a three-alpha helix bundle packed against a three-stranded beta-sheet. Comparing with analogous WH domains, this one presents an additional helix and helix H3 is not positively charged as in classical DNA-binding WH domains. KIN17 is a highly conserved protein that participates in DNA replication, DNA repair and cell cycle progression.
Pfam PF23824: Family of unknown function (DUF7194) (family)
This entry represents an uncharacterized protein family found in viruses from the order Caudoviricetes. The family contains proteins between 199 and 219 amino acids in length. The function of this family 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 PF22102: ElaD/SseL-like C-terminal (domain)
This entry represents the C-terminal catalytic domain from a group of CE proteases from human pathogens including ElaD from E.coli, SseL from Salmonella typhimurium and ShiCE from Shigella, which are dedicated deubiquitinases (DUBs), proteases that reverse the addition of ubiquitin to substrates, and effectively hijacks the host's ubiquitination processes.
Pfam PF13896: Glycosyl-transferase for dystroglycan (domain)
This glycosyl-transferase brings about the glycosylation of the alpha-dystroglycan subunit. Dystroglycan is an integral member of the skeletal muscular dystrophin glycoprotein complex, which links dystrophin to proteins in the extracellular matrix.
Pfam PF15164: Williams-Beuren syndrome chromosomal region 28 protein homologue (family)
WBS28 is an integral membrane family. These proteins have been identified as being linked to Williams-Beuren syndrome, OMIM:194050.  This family of proteins is found in eukaryotes, and are typically 266 amino acids in length.
Wikipedia: Williams syndrome (WS), also Williams–Beuren syndrome (WBS), is a genetic disorder that affects many parts of the body. Facial features frequently include a broad forehead, underdeveloped chin, short nose, and full cheeks. Mild to moderate intellectual disability is observed, particularly challenges with visual spatial tasks such as drawing. Verbal skills are relatively unaffected. Many people have an outgoing personality, an openness to engaging with other people, and a happy disposition. Medical issues with teeth, heart problems, and periods of high blood calcium are common.
Pfam PF02667: Short chain fatty acid transporter (family)
This family consists of two sequences annotated as short chain fatty acid transporters, however, there are no references giving details of experimental characterisation of this function.
Pfam PF09875: Uncharacterized protein conserved in archaea (DUF2102) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08777: RNA binding motif (domain)
This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.
Pfam PF09192: Actin-fragmin kinase, catalytic (domain)
Members of this family assume a secondary structure consisting of eight beta strands and 11 alpha-helices, organised in two lobes. They are predominantly found in actin-fragmin kinase, where they act as a catalytic domain that mediates the phosphorylation of actin.
Pfam PF16771: Regulator of Ty1 transposition protein 107 BRCT domain (domain)
This is the sixth BRCT domain of regulator of Ty1 transposition protein 107 (RTT107). It is involved in binding phosphorylated histone H2A.
Pfam PF12178: Chromosome passenger complex (CPC) protein INCENP N terminal (domain)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N terminal domain is the domain involved in formation of this three helical bundle.
Wikipedia: Inner centromere protein is a protein that in humans is encoded by the INCENP gene. It is a regulatory protein in the chromosome passenger complex (CPC). It is involved in regulation of the catalytic proteins Aurora B and Aurora C. It acts in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N-terminal domain of INCENP is the domain involved in formation of this three-helical bundle while its C-terminal domain is responsible for the interaction with Aurora B.
Pfam PF14801: TrmI-like N-terminal (domain)
This is the N-terminal domain of tRNA (adenine(58)-N(1))- methyltransferase TrmI, a subunit of the tRNA methyltransferase complex that is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. The exact function of the N-terminus is not known but it is necessary for maintaining the overall folding and for full enzymatic activity.
Pfam PF24937: Domain of unknown function (DUF7754) (domain)
This is a presumed domain found at the C-terminal of worm proteins. It may be related to BACK domains.
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 PF03540: Transcription initiation factor TFIID 23-30kDa subunit (family)
Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses  to various activators and repressors. The complex includes TATA  binding protein (TBP) and various TBP-associated factors (TAFS).  TFIID is a bona fide RNA polymerase II-specific TATA-binding  protein-associated factor (TAF) and is essential for viability.  This entry represents one of the TAFs, TAF10. TFIID acts to nucleate the transcription complex, recruiting the  rest of the factors through a direct interaction with TFIIB. The TBP  subunit of TFIID is sufficient for TATA-element binding and TFIIB  interaction, and can support basal transcription. TAF10 is part of other transcription regulatory multiprotein  complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC],  STAGA, and PCAF/GCN5). Several TAFs interact via histone-fold  motifs. The histone fold (HFD) is the interaction motif involved in  heterodimerisation of the core histones and their assembly into  nucleosome octamer. The minimal HFD contains three alpha-helices  linked by two loops. The HFD is found in core histones, TAFs and  many other transcription factors. Five HF-containing TAF pairs have  been described in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.
Wikipedia: The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
Pfam PF01464: Transglycosylase SLT domain (domain)
This family is distantly related to [pfam:PF00062]. Members are found in phages, type II, type III and type IV secretion systems (reviewed in).
Pfam PF02413: Caudovirales tail fibre assembly protein, lambda gpK (family)
This family contains bacterial and phage tail fibre assembly proteins. E.coli contains several members of this family although the function of these proteins is uncertain. Using the lambda phage members as examples, there are both gptfa and gpK tail proteins here.  GpK forms part of the TTC or tail-tip complex that is located at the distal end of the tail. TTCs form the platform on which the tail-tube proteins self-assemble and are also the attachment point for fibres or receptor-binding proteins that mediate phage-adsorption to the surface of the host cell. TTC assembly starts with gpJ, which is also known as the central tail fibre and is involved in host-cell adsorption. It is the C-terminus of gpJ that interacts with the lamB receptor on host cells. A number of intermediates including gpK then interact with gpJ during tail morphogenesis.
Pfam PF24368: Family of unknown function (DUF7524) (family)
This family includes a group of proteins from archaea. Members are predicted to be organised into two domains, an N-terminal with an all-beta configuration and a C-terminal with a mainly alpha-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 PF12330: Haspin like kinase domain (family)
This family represents the haspin-like kinase domains.
Pfam PF24258: Domain of unknown function (DUF7459) (domain)
This entry represents an uncharacterised protein domain found in a mycobacterial phage proteins. These domains form a zinc binding cluster where 8 cysteine and histidine residues bind two zinc ions according to structure prediction (iPTM=0.87).
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 PF16417: CCR4-NOT transcription complex subunit 1 TTP binding domain (repeat)
This is the TTP binding domain of CCR4-NOT transcription complex subunit 1. It adopts a MIF4G (middle portion of eIF4G) fold.
Wikipedia: CCR4-NOT transcription complex subunit 1 is a protein that in humans is encoded by the CNOT1 gene.
Pfam PF17899: Peptidase M61 N-terminal domain (domain)
This domain is found at the N-terminus of [pfam:PF05299] and has a beta sandwich-like fold with similarity to the baculovirus p35 protein.
Pfam PF04727: ELMO/CED-12 family (family)
This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the C. elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells. ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment.
Wikipedia: ELMO is a family of related proteins (~82 kDa) involved in intracellular signalling networks. These proteins have no intrinsic catalytic activity and instead function as adaptors which can regulate the activity of other proteins through their ability to mediate protein-protein interactions.
Pfam PF15990: UPF0767 family (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between  and 92 amino acids in length. There are two conserved sequence motifs: IGYN and SPSL.
Pfam PF18270: Virulence factor Evf (domain)
This domain is found in Erwinia virulence factor (Evf) present in the Drosophila Pathogen, Erwinia carotovora. Evf is able to bind to model membranes containing negatively charged phospholipids and to promote their aggregation. Palmitoic acid covalently binds to the completely conserved Cys209. The structure of Evf is unlike any virulence factors known to date.
Pfam PF24064: GATOR1 complex protein NPRL3, C-terminal HTH (domain)
This domain is found at the C-terminal end of human GATOR1 complex protein NPRL3 (NPRL3) and similar proteins mainly found in animal and fungi. As a component of the GATOR1 complex, NPRL3 functions as an inhibitor of the amino acid-sensing branch of the mTORC1 pathway. This domain shows an helix-turn-helix (HTH) configuration.
Pfam PF20708: Family of unknown function (DUF6822) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes (predominantly in the Dinoflagellate Symbiodinium microadriaticum). There are several highly conserved W residues.
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 PF00142: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family (domain)
This entry includes the bacterial nitrogenase iron protein NifH , chloroplast encoded chlL (or frxC) , and archaeal Ni-sirohydrochlorin a,c-diamide reductive cyclase complex component CfbC .

Nitrogenase (1.18.6.1) is responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 1 which contains the active site for the reduction of nitrogen to ammonia and component 2 (also called the iron protein) . Component 2 is a homodimer of a protein (gene nifH) which binds a single 4Fe-4S iron sulfur cluster. In the nitrogen fixation process NifH is first reduced by a protein such as ferredoxin; the reduced protein then transfers electrons to component 1 with the concomitant consumption of ATP .

There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) and in the central section there are two conserved cysteines which have been shown, in NifH, to be the ligands of the 4Fe-4S cluster.

Protochlorophyllide reductase is involved in light-independent chlorophyll biosynthesis. The light-independent reaction uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This enzyme complex is composed of three subunits: ChlL, ChlN and ChlB. ChlL (also known as frxC) is present as a homodimer, and binds one 4Fe-4S cluster per dimer. The conserved domains, including the ATP-binding motif and the Fe-S binding motif found in the three subunits, are similar to those in nitrogenases .
Pfam PF14530: Domain of unknown function (DUF4439) (domain)
This domain has a ferritin-like fold.
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 PF05957: DUF883 N-terminal domain (domain)
This family consists of several hypothetical bacterial proteins of unknown function. The N-terminal domain found in this entry is related to [pfam:PF05532].
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 PF14620: YpeB sporulation, PepSY1 and PepSY2 domains (domain)
YpeB is a sporulation protein that, together with the spore-cortex-lytic enzyme SleB, is required for normal germination. YpeB stabilises SleB enzyme and may regulate its activity during spore germination. It consists of three tandemly repeated PepSY domains at the C-terminal, being the first two (PepSY1 and PepSY2) represented in this entry and the last one in [pfam:PF03413].
Pfam PF20470: Helix-turn-helix domain (domain)
This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta.
Pfam PF00289: Biotin carboxylase, N-terminal domain (domain)
This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes, and propionyl-CoA carboxylase A chain.
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 PF20355: Family of unknown function (DUF6650) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 175 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 PF21775: PutA, RHH domain (domain)
This domain is found in the Bifunctional protein PutA from Escherichia coli and similar sequences mainly found in proteobacteria. PutA is both a bifunctional proline catabolic enzyme that oxidises proline to glutamate for use as a carbon and nitrogen source and an autogenous transcriptional repressor of the put operon. This entry represents the N-terminal ribbon-helix-helix (RHH) domain, which consists of a beta-strand and two alpha-helices. This domain has a Lys at the end of the beta-strand that interacts directly with DNA bases through the major groove, contributing to transcriptional regulation.
Pfam PF01850: PIN domain (domain)
PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation . PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay  and in processing of 18S ribosomal RNA . In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin .
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 PF05068: Mannitol repressor (family)
The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (MtlA) and mannitol phosphate dehydrogenase (MtlD) contains an additional downstream open reading frame which encodes the mannitol repressor (MtlR).
Pfam PF15226: HCF-1 beta-propeller-interacting protein family (family)
HPIP is a small cellular polypeptide that binds to the beta-propeller domain of HCF-1. HPIP regulates HCF-1 activity by modulating its subcellular localisation. HCF-1 is a cellular protein required by VP16 to activate the herpes simplex virus- immediate-early genes. VP16 is a component of the viral tegument and, after release into the cell, binds to HCF-1 and translocates to the nucleus to form a complex with the POU domain protein Oct-1 and a VP16-responsive DNA sequence. HPIP-mediated export may provide the pool of cytoplasmic HCF-1 required for import of virion-derived VP16 into the nucleus.