SII-SWORD/CoKE huggingface dataset:
Pfam PF13113: Protein of unknown function (DUF3970) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved NPKY sequence motif.
Pfam PF02841: Guanylate-binding protein, C-terminal domain (domain)
Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.
Wikipedia: In molecular biology, the guanylate-binding proteins family is a family of GTPases that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-KD immunity-related GTPases (IRGs), the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class.
Pfam PF04693: Archaeal putative transposase ISC1217 (family)
Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families . This family includes the putative transposase ISC1217 from archaebacteria.
Pfam PF02405: Permease MlaE (family)
MlaE is a permease which in E. coli is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. In [swissprot:Q7DD59] it is involved in L-glutamate import into the cell. In [swissprot:Q8L4R0] it is involved in lipid transfer within the cell.
Pfam PF19799: Family of unknown function (DUF6282) (family)
This family of proteins is functionally uncharacterised and it is found in bacteria and archaea. Proteins in this family are typically between 280 and 313 amino acids in length. This family has some overlaps with families from the clan CL0034.
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 PF18585: Chromatin remodeling factor Mit1 C-terminal Zn finger 2 (domain)
The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins. The Mit1 C terminus contains two zinc binding motifs (CCHC zinc fingers) at the C-terminus onto which the alpha helices from both Clr1 and Mit1 pack. The Mit1 chromatin remodeler uses its C-terminal domain to intimately bind to the N-terminal half of Clr1 to integrate into the SHREC complex. This is entry represents the second C-terminal zinc-binding domain found on Mit-1.
Pfam PF15681: Lymphocyte activation family X (family)
LAX is a family of proteins is found in chordates. LAX is membrane-associates and expressed in B cells, T cells, and other lymphoid-specific cell types. It down-regulates antigen-receptor signalling in T cells by inhibiting TCR-mediated p38 MAPK activation.
Pfam PF07276: Apopolysialoglycoprotein (PSGP) (repeat)
This family represents a series of 13 reside repeats found in the apopolysialoglycoprotein of Oncorhynchus mykiss (Rainbow trout) and Oncorhynchus masou (Cherry salmon). Polysialoglycoprotein (PSGP) of unfertilised eggs of rainbow trout consists of tandem repeats of a glycotridecapeptide, Asp-Asp-Ala-Thr*-Ser*-Glu-Ala-Ala-Thr*-Gly-Pro-Ser- Gly (* denotes the attachment site of a polysialoglycan chain). In response to egg activation, PSGP is discharged by exocytosis into the space between the vitelline envelope and the plasma membrane, i.e. the perivitelline space, where the 200-kDa PSGP molecules undergo rapid and dramatic depolymerisation by proteolysis into glycotridecapeptides.
Pfam PF13578: Methyltransferase domain (domain)
This family appears to be a methyltransferase domain.
Pfam PF09429: WW domain binding protein 11 (family)
The WW domain is a small protein module with a triple-stranded beta-sheet fold.  This is a family of WW domain binding proteins.
Pfam PF17508: Microcin V bacteriocin (family)
Family members are bacterial microcin-V peptides MccV, also known as colicin V. MccV was the first antibiotic substance reported to be produced by E. coli. This antibacterial agent was initially named colicin V (ColV). However, on account of several characteristics (low molecular mass, non-inducible production, and dedicated export system), it became classified within the microcins. The structural gene cvaC, encodes the 103-aa MccV precursor. The dedicated export system of MccV has been well characterized and involves two genes that form the second operon. The MccV protein has an N-terminal double glycine motif which precedes the cleavage site for the precursor protein.
Pfam PF23993: Domain of unknown function (DUF7311) (domain)
This domain is found in uncharacterised archaeal 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 PF06233: Usg-like family (family)
Family of bacterial proteins, referred to as Usg. Usg is found in the same operon as trpF, trpB, and trpA and is expressed in a coupled transcription-translation system.
Pfam PF21169: Fanconi-associated nuclease 1, SAP subdomain (domain)
This domain is found in Fanconi-associated nuclease 1 from humans (Fan1) and similar proteins from chordates. Fan1 is involved in the processing of DNA interstrand crosslinks (ICLs) and therefore in the maintenance of genomic stability and prevention of tissue decline in multiple organs. FAN1 consists of an SAP-containing N-terminal domain, a middle tetratricopeptide repeat domain (TPR) and a C-terminal viral replication and repair nuclease domain (VRR_nuc domain, [pfam:PF08774]). This entry represents the SAP subdomain, part of the N-terminal domain. It consists of four alpha-helices.
Pfam PF03887: YfbU domain (domain)
This presumed domain is about 160 residues long.  It is found in archaebacteria and eubacteria.  In [swissprot:Q9EUM2] it is associated with a helix-turn-helix domain. This suggests that this may be a ligand binding domain.
Pfam PF14838: Integrator complex subunit 5 C-terminus (family)
This family of proteins represents the C-terminus of subunit 5 of the integrator complex involved in snRNA transcription and processing.
Pfam PF23327: ATPase MORC2, chromo domain-like (domain)
This domain is found in human ATPase MORC2 and similar sequences predominantly found in vertebrates. MORC2 is essential for epigenetic silencing by the HUSH (human silencing hub) complex. This domain, which is predicted to adopt an alpha-beta configuration, is often found associated with [pfam:PF13589], [pfam:PF17942] and [pfam:PF07496].
Pfam PF09711: CRISPR-associated protein (Cas_Csn2) (family)
CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins found only in CRISPR-containing species, near other CRISPR-associated proteins (cas). The species range so far for these proteins is pathogenic bacteria only. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats).
Pfam PF07262: CDI immunity protein (family)
CdiI immunity proteins function as part of the bacterial contact-dependent growth inhibition (CDI) system. CDI is mediated by the CdiB-CdiA two-partner secretion system. Each CdiA protein  exhibits a distinct growth inhibition activity, which resides in the polymorphic C-terminal region (CdiA-CT). Cells with the CDI sytem also express a CdiI immunity protein that blocks the activity of cognate CdiA-CT, thereby protecting the cell from autoinhibition. In many CDI systems the cdiBAI genes are followed by orphan cdiA-CT/cdiI modules, suggesting that these modules are  exchanged between the CDI systems of different bacteria.
Pfam PF01743: Poly A polymerase head domain (domain)
This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA [ec:2.7.7.19]. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA [ec:2.7.7.25]. This family is part of the nucleotidyltransferase superfamily.
Pfam PF17197: Domain of unknown function (DUF5134) (family)
Proteins in this family are uncharacterised, but have been identified as members of a gene cluster for the synthesis of the tetramic-acid  antibiotic streptolydigin, which inhibits bacterial RNA polymerase  (RNAP).
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 PF10642: Mitochondrial import receptor subunit or translocase (family)
This protein family is very short and is only found in yeasts. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore. Deletion of the C-terminal transmembrane domain of Tom5 interfered with phosphatidylserine (PS) transfer to mitochondria and disrupted mitochondrial function.
Pfam PF24077: Immunoglobulin A1 protease autotransporter domain 2 (domain)
This entry represents what has been called domain 2 of immunoglobulin A1 protease autotransporter (IgA0) from bacteria. These proteases serve as virulence factors by cleaving IgA of humans and great apes. This domain has been suggested to be involved in protein-protein interactions and may contribute to substrate recognition by forming binding surface for IgA.
Pfam PF16323: Domain of unknown function (DUF4959) (family)
This family consists of uncharacterised proteins around 400 residues in length and is mainly found in various Bacteroides, Pedobacter and Parabacteroides species. Several proteins are annotated as Galactose-binding like proteins, but the specific function of this protein is unknown.
Pfam PF23080: Domain of unknown function (DUF7046) (domain)
This domain is found in a group of uncharacterised plant proteins. These proteins are probably distantly related to the plant-specific actin-binding protein SCAB1 and are predicted to contain a fusion domain composed of Ig and PH-like domains in a similar arrangement as in SCAB1 (([pfam:PF16709]) and ([pfam:PF17684])). The domain represented by this entry corresponds to an atypical PH-like domain.
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 PF03491: Serotonin (5-HT) neurotransmitter transporter, N-terminus (family)
This short domain lies at the very N-terminus of many serotonin and other transporter proteins, eg SNF, [pfam:PF00209].
Pfam PF12324: Helix-turn-helix domain of alkylmercury lyase (domain)
Alkylmercury lyase ([ec:4.99.1.2]) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with [pfam:PF03243].
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF01601: Coronavirus spike glycoprotein S2 (family)
The coronavirus spike glycoprotein forms the characteristic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 [pfam:PF01600] and S2,. The S2 subunit normally contains multiple key components, including one or more fusion peptides (FP), a second proteolytic site (S2') and two conserved heptad repeats (HRs), driving membrane penetration and virus-cell fusion. The HRs can trimerize into a coiled-coil structure built of three HR1-HR2 helical hairpins presenting as a canonical six-helix bundle and drag the virus envelope and the host cell bilayer into close proximity, preparing for fusion to occur.
Pfam PF13239: 2TM domain (family)
This short region contains two transmembrane alpha helices that are found associated with a wide range of other domains.  This domain may be involved in cell lysis or peptidoglycan turnover.
Pfam PF09443: Cripto_Frl-1_Cryptic (CFC) (domain)
CFC domain is one half of the membrane protein Cripto, a protein overexpressed in many tumours and structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2.  CFC is approx 40-residues long, compacted by three internal disulphide bridges, and binds Alk4 via a hydrophobic patch. CFC is structurally homologous to the VWFC-like domain.
Wikipedia: In molecular biology, the CFC domain is a protein domain found at the C-terminus of a number of proteins including Cripto. It is structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2. CFC is approx 40-residues long, compacted by three internal disulphide bridges, and binds Alk4 via a hydrophobic patch. CFC is structurally homologous to the VWFC-like domain.
Pfam PF24638: DEAH11 eukaryotic type KH-domain (domain)
This domain is found in the ATP-dependent RNA helicase DEAH11, DEAH12 from Arabidopsis thaliana and related plant proteins. This domain shares detectable similarity to type I KH domains and is predicted to adopt an alpha/beta structure with similar topology.
Pfam PF09603: Fibrobacter succinogenes major domain (Fib_succ_major) (domain)
This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulfide bond formation, are also consistent with an extracytoplasmic location for this domain. This domain can also be found in small numbers of proteins in Chlorobium tepidum and Bacteroides thetaiotaomicron.
Pfam PF15421: Putative polysaccharide deacetylase (family)
This entry represents a group of putative polysaccharide deacetylases from bacteria, mainly from Bacteroidales.
Pfam PF15890: Putative zinc-binding metallo-peptidase (family)
This family is a putative zinc-binding metallo-peptidase. There are two highly conserved motifs, HHExxH and ED. HExxH with ED is indicative of zinc-binding metallo-peptidases.
Pfam PF23593: Serine/threonine-protein kinase ATR-like, HEAT repeats (repeat)
This region of HEAT repeats is found in human Serine/threonine -protein kinase ATR and similar eukaryotic proteins. ATR acts as a DNA damage sensor and is associated with severe disorders such as Seckel syndrome 1. This protein is organised into a large N-terminal alpha solenoid containing HEAT repeats, a FAT (FRAP, ATM, TRRAP) domain, a kinase domain ([pfam:PF00454]), and a C-terminal short segment referred to as FATC ([pfam:PF02260]). The FAT domain contains TPR (tetratricopeptide) repeats ([pfam:PF02259]) followed by a HEAT repeat domain (this entry).
Pfam PF15433: Mitochondrial 28S ribosomal protein S31 (family)
MRP-S31 is the mitochondrial 28S ribosomal subunit S31. This family of proteins is found in eukaryotes. Proteins in this family are typically between 246 and 395 amino acids in length. There are two conserved sequence motifs: RHFMELV and GLSKN.
Pfam PF16760: Starch/carbohydrate-binding module (family 53) (family)
This entry represents CBM25, which has been shown to bind starch .
A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF22539: Family of unknown function (DUF7004) (family)
This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 160 amino acids in length. They are predicted to adopt globular alpha/beta structure. These proteins contain two highly conserved sequence motifs GxFDxWC and KRxKRLG that may be of functional importance.
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 PF21278: YlmH, N-terminal (domain)
This is a domain found at the N-terminal of the Putative RNA-binding protein YlmH.
Pfam PF06092: Enterobacterial putative membrane protein (DUF943) (family)
This family consists of several hypothetical putative membrane proteins from Escherichia coli, Yersinia pestis and Salmonella typhi. Recently, it was proposed that members of this family along with members of DUF3289 ([pfam:PF11692]) should be recognised as a putative toxin-antitoxin pair in which DUF3289 ([pfam:PF11692]) is a homolog of Colicin M and DUF943 acts as its cognate immunity protein.
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 PF01538: Hepatitis C virus non-structural protein NS2 (family)
The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases.  Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.
Pfam PF00071: Ras family (domain)
Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See [pfam:PF00009] [pfam:PF00025], [pfam:PF00063]. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
Wikipedia: Ras, from "Rat sarcoma virus", is a family of related proteins that are expressed in all animal cell lineages and organs. All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells. Ras is the prototypical member of the Ras superfamily of proteins, which are all related in three-dimensional structure and regulate diverse cell behaviours.
Pfam PF14908: CCDC81 eukaryotic HU domain 1 (domain)
This is the first of two HU domains found in the CCDC81-like proteins. CCDC81 has been experimentally linked to the centrosome; eukaryotic CCDC81 HU domains are predicted to function in protein-protein interactions in centrosome organization and potentially contribute to cargo-binding in conjunction with Dynein-VII. A striking lineage-specific expansion of the domain is observed in birds, where the HU domains could function in recognition of non-self molecules.
Pfam PF20877: Alpha-beta plait domain in TMEM16 lipid scramblase (domain)
This entry represents an alpha-beta plait domain from a group of fungal TMEM16 family of proteins, also known as anoctamins, including SwissProt:Q4WA18 from Aspergillus fumigatus and ist2 from S.pombe. Proteins in this entry operate as Ca2+-activated lipid scramblases. This domain may play a role in dimerisation, although its precise function is uncertain.
Pfam PF13321: Domain of unknown function (DUF4084) (family)
This family of Firmicute proteins is frequently associated with the EAL, GGDEF and PAS families, [pfam:PF00563], [pfam:PF00990], and [pfam:PF00989]. The exact 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 PF09918: Uncharacterized protein containing a ferredoxin domain (DUF2148) (family)
This domain, found in various hypothetical bacterial proteins containing a ferredoxin domain, 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.