SII-SWORD/CoKE huggingface dataset:
Pfam PF18982: Wadjet protein JetA (family)
This family includes Wadjet protein JetA, a component of anti plasmid transformation system Wadjet type I, composed of JetA, JetB, JetC and JetD. Expression of Wadjet type I in B.subtilis (strain BEST7003) reduces the transformation efficiency of plasmid pHCMC05.
Pfam PF00005: ABC transporter (domain)
ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes.  ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain [pfam:PF00664]. These four domains may belong to a single polypeptide as in [swissprot:P13569], or belong in different polypeptide chains.
Wikipedia: The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
Pfam PF03148: Tektin family (family)
Tektins are cytoskeletal proteins. They have been demonstrated in such cellular sites as centrioles, basal bodies, and along ciliary and flagellar doublet microtubules. Tektins form unique protofilaments, organised as longitudinal polymers of tektin heterodimers with axial periodicity matching tubulin. Tektin polypeptides consist of several alpha-helical regions that are predicted to form coiled coils. Indeed, tektins share considerable structural similarities with intermediate filament proteins. Possible functional roles for tektins are: stabilisation of tubulin protofilaments; attachment of A and B-tubules in ciliary/flagellar microtubule doublets and C-tubules in centrioles; binding of axonemal components. More recent structural work suggests that tektins and intermediate filaments to be structurally distinct classes of cytoskeletal filaments.
Wikipedia: Tektins are cytoskeletal proteins found in cilia and flagella as structural components of outer doublet microtubules. They are also present in centrioles and basal bodies. They are polymeric in nature, and form filaments.
Pfam PF10256: Golgin subfamily A member 7/ERF4 family (domain)
This family of proteins includes Golgin subfamily A member 7 proteins as well as Ras modification protein ERF4.
Pfam PF14378: PAP2 superfamily (family)
This entry includes a group of inositolphosphotransferases, including inositol phosphorylceramide synthase catalytic subunit Aur1 and inositolphosphotransferase 1 (Ipt1) from S. cerevisiae. Aur1 is a catalytic component of the inositol phosphorylceramide synthase which catalyses the addition of a phosphorylinositol group onto ceramide to form inositol phosphorylceramide, an essential step in sphingolipid biosynthesis . Ipt1 is involved in synthesis of mannose-(inositol-P)2-ceramide (M(IP)2C), the most abundant and complex sphingolipid in S. cerevisiae . This entry also includes some uncharacterised archaeal and bacterial proteins.
Pfam PF11620: GA-binding protein alpha chain (family)
This family of proteins represents the transcription factor GABP alpha. This alpha domain is a five-stranded beta-sheet crossed by a distorted helix termed an OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300, a direct link between GABP and transcriptional machinery has been made.
Pfam PF06047: NF-kappa-B-activating protein C-terminal domain (domain)
This is the C-terminal domain found in NF-kappa-B-activating protein (Nkap) and a hypothetical open reading frame on chromosome 6, c6orf194. Functional studies in Nkap indicate that this domain is the HDAC3 binding domain and is required for transcriptional repression. Nkap functions as a transcriptional repressor on Notch target genes, and is required for T cell development and acquisition of functional competency.
Pfam PF02890: Borrelia family of unknown function DUF226 (family)
This family of proteins are found in Borrelia.  The proteins are about 190 amino acids long and have 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 PF04472: Cell division protein SepF (family)
SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This family also includes archaeal related proteins of unknown function.
Pfam PF05689: Adhesion domain (domain)
This entry represents the Adhesion domain found in InvasinE (invE). Invasins are members of the inverse autotransporter (IAT) family also referred to as type Ve secretion system. In general, they consist of an N-terminal beta-barrel-like domain, which is responsible for attachment of invasin to the outer membrane region of bacteria, repetitive Immunoglobulin-like (Ig) domains, which vary significantly in number among all the invasins, and the C-terminal domain/adhesion domain (AD), which provides invasins with the specificity to bind to its host target molecules. InvE-AD adopts a C-type lectin-like domain (CTLD)fold with unique modifications. The core structure of the adhesion domain (AD) is made up of a globular alpha/beta fold and can be divided into three sub-sections. The first is a lasso-shaped loop structure termed the "adaptor ring" since it forms a ring-shaped platform that connects BIg21 [pfam:PF05688] with the two residual sub-sections in the AD. These two residual subsections are the "C-type lectin-like domain" and the "wedge module". InvE-CTLD lacks the ability to coordinate Ca2+, and motifs such as EPN, QPD, and WND that are responsible for the specificity of carbohydrate recognition are also absent, giving rise to the notion that the InvE-CTLD is not a carbohydrate binding domain.
Pfam PF23858: Family of unknown function (DUF7220) (family)
This short protein is found among some phage. It is possibly distantly related to the small terminase family [pfam:PF05119].
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 PF03097: BRO1-like domain (repeat)
This domain is found in a number proteins including Rhophilin [swissprot:Q61085] and BRO1 [swissprot:P48582].  It is known to have a role in endosomal targeting.  ESCRT-III subunit Snf7 binds to a conserved hydrophobic patch in the BRO1 domain that is required for protein complex formation and for the protein-sorting function of BRO1.
Pfam PF20454: Terminase large subunit gpA, endonuclease domain (domain)
Terminase enzymes mediate the packaging viral DNA into an empty procapsid in a process called DNA packaging and are composed of a heterotrimeric complex of a large subunit (TerL, gpA) and the small subunit (TerS, gpNu1) (TerL-TerS2). TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity. This entry represents the endonuclease domain found at the C-terminal of Terminase large subunit (GpA) from Bacteriophage lambda, which excises an individual genome from the concatemer at the cos site.
Pfam PF17564: Family of unknown function (DUF5470) (family)
This is a family of unknown function found in viruses.
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 PF14245: Type IV pilin PilA (family)
This family consists of proteins which form type IV pili. In M. xanthus these pili are required for social motility.
Pfam PF05154: TM2 domain (domain)
This family is composed of a pair of transmembrane alpha helices connected by a short linker.  The function of this domain is unknown, however it occurs in a wide range or protein contexts.
Pfam PF12783: Mon2/Sec7/BIG1-like, HUS domain (repeat)
The full-length Sec7 functions proximally in the secretory pathway as a protein binding scaffold for the coat protein complexes COPII-COPI. The COPII-COPI-protein switch is necessary for maturation of the vesicular-tubular cluster, VTC, intermediate compartments for Golgi compartment biogenesis. This N-terminal domain however does not appear to be binding either of the COP or the ARF. This is the HUS (homology upstream of Sec7) domain of Sec7 and related proteins such as protein Mon2 and BIG1-like proteins, which plays a regulatory role together with DCB domain ([pfam:PF16213]).
Pfam PF11574: Resuscitation-promoting factor Rpf1, C-terminal (domain)
This is the C-terminal domain of Resuscitation-promoting factor Rpf1 from Corynebacterium glutamicum, which is adjacent the RPF domain ([pfam:PF06737]). The function of this domain is not yet known. Rpf1 has peptidoglycan hydrolytic activity and stimulates resuscitation of dormant cells.
Pfam PF03254: Xyloglucan fucosyltransferase (family)
Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue.
Pfam PF21651: Family of unknown function (DUF6858) (domain)
This family of proteins are distantly related to [pfam:PF03625]. Their function is as yet 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 PF09971: Predicted membrane protein (DUF2206) (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 PF08326: Acetyl-CoA carboxylase, central region (family)
The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain ([pfam:PF01039]). This enzyme ([ec:6.4.1.2]) is involved in the synthesis of long-chain fatty acids, as it catalyses the rate-limiting step in this process.
Pfam PF05512: AWPM-19-like family (family)
Members of this family are 19 kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid.  The increase presence of this protein leads to greater tolerance of freezing.
Pfam PF15406: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF06579: Caenorhabditis elegans ly-6-related protein (family)
This family consists of several Caenorhabditis elegans specific ly-6-related HOT and ODR proteins. These proteins are involved in the olfactory system. Odr-2 mutants are known to be defective in the ability to chemotax to odorants that are recognised by the two AWC olfactory neurons. Odr-2 encodes a membrane-associated protein related to the Ly-6 superfamily of GPI-linked signaling proteins.
Pfam PF07781: Reovirus minor core protein Mu-2 (family)
This family represents the Reovirus core protein Mu-2. Mu-2 is a microtubule associated protein and is thought to play a key role in the formation and structural organisation of reovirus inclusion bodies.
Pfam PF07930: D-aminopeptidase, domain B (domain)
D-aminopeptidase ([swissprot:Q9ZBA9]) is a dimeric enzyme with each monomer being composed of three domains. Domain B is organised to form a beta barrel made up of eight antiparallel beta strands. It is connected  to domain A, the catalytic domain, by an eight-residue sequence, and also interacts with both domains A and C  via non-covalent bonds. Domain B probably functions in maintaining domain C in a good position to interact with domain A.
Wikipedia: In molecular biology, D-stereospecific aminopeptidase (D-aminopeptidase) EC 3.4.11.19 is an enzyme which catalyses the release of an N-terminal D-amino acid from a peptide, Xaa-|-Yaa-, in which Xaa is preferably D-Ala, D-Ser or D-Thr. D-amino acid amides and methyl esters also are hydrolyzed, as is glycine amide.
Pfam PF08996: DNA Polymerase alpha zinc finger (domain)
The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain.
Pfam PF23791: Family of unknown function (DUF7173) (domain)
This family contains a set of uncharacterized proteins found predominantly in viruses, particularly bacteriophages. The proteins are typically 130-150 amino acids in length. AlphaFold models of this family show some weak partial structural similarity to the Recombination-associated protein RdgC.
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 PF02169: LPP20 lipoprotein (family)
This family contains the LPP20 lipoprotein, which is a non-essential class of lipoprotein.
Pfam PF19177: Family of unknown function (DUF5859) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses.
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 PF12352: Snare region anchored in the vesicle membrane C-terminus (domain)
Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle [pfam:PF05008].
Pfam PF17583: Family of unknown function (DUF5484) (family)
This is a family of unknown function found in Myoviridae.
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 PF23454: Transcriptional regulator Brz zinc beta ribbon domain (domain)
This domain is found in a group of small proteins mainly from Halobacteria including Transcriptional regulator Brz. Brz is known to activate transcription of bacteriorhodopsin and phytoene synthase. It may interact with DNA or RNA via the zinc finger domain. This domain is predicted to adopt a zinc beta ribbon fold in which the last zinc coordinating residue is histidine instead of the commonly found cysteine. This kind of substitution has been already observed in other zinc beta ribbon domains from transcription factors, methytransferases and ribosomal proteins. Mutation of the cysteine and histidine residues has a pronounced effect on the Brz function.
Pfam PF24316: T6SS Tli3 immunity protein (domain)
This entry represents the type VI secretion system (T6SS) Tli3 immunity protein from adherent-invasive Escherichia coli and related proteins. Tli3 is an outer membrane lipoprotein and a cognate immunity protein of T6SS Tle3 phospholipase effector. Tli3 and Tle3 form a stable complex in which a loop of Tli3 inserts deeply in the Tle3 substrate-binding pocket and thus inhibiting its function. Tli3 folds into an all-beta structure composed of three stacked beta-sheets, two of which are resembling a beta-sandwich while the third packs on its edge.
Pfam PF25037: Intermembrane lipid transfer protein VPS13, C-terminal (domain)
This entry represents the C-terminal PH-like domain from VPS13 which weakly binds to phosphatidylinositol 4,5-bisphosphate and contributes to membrane recruitment. Truncation of this domain in VPS13A are causative for chorea-acanthocytosis, which suggests that it plays an important function.
Pfam PF03889: Alternative ribosome-rescue factor A (domain)
During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly known as YaeJ) are present in many bacterial species. Family members such as ArfA cooperates with the canonical peptide release factor RF2 to hydrolyse the peptidyl-tRNA in the non-stop complex. Structural and biochemical analysis show that ArfA anchors its positively charged C-terminal in the mRNA entry channel of the ribosome. Whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2 thereby triggering RF2 peptidyl-hydrolysing activity.
Pfam PF09151: Domain of unknown function (DUF1936) (domain)
This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon 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 PF12205: G protein-coupled receptor kinase-interacting protein 1 C term (domain)
This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF01412], [pfam:PF00023], [pfam:PF08518]. GIT1 plays an important role in cell adhesion, motility, cytoskeletal remodelling and membrane trafficking. To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C terminal and the LD motifs of paxillin. The C terminal folds into a four helix bundle.
Pfam PF22213: CPV, RNA-directed RNA polymerase, C-terminal (domain)
This domain is found at the C-terminal of RNA-directed RNA polymerase (RdRP) from Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) and similar sequences from reovirus. This protein adopts a closed cage-like structure consisting of a central polymerase domain sandwiched between N-terminal and C-terminal bracelet domains. This domain adopts a predominantly alpha-helical configuration.
Pfam PF20404: Family of unknown function (DUF6694) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 109 and 273 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 PF07943: Penicillin-binding protein 5, C-terminal domain (domain)
Penicillin-binding protein 5 expressed by E. coli ([swissprot:P04287]) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain ([pfam:PF00768]) is the catalytic domain.  The C-terminal domain featured in this family is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides.
Pfam PF19975: Double-GTPase 1 (domain)
GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs to a previously unrecognised family of the TRAFAC clade with a conserved glutamate in its Walker B motif.
Pfam PF04815: Sec23/Sec24 helical domain (domain)
COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices.
Pfam PF23798: SPT8 beta propeller (repeat)
This entry represents the beta-propeller found in Transcription factor SPT8 (SPT8) from fungi. SPT8 is a member of the transcription regulatory histone acetylation (HAT) complex SAGA. SPT8 interacts with TATA-binding protein (TBP) acting as a suppressor of transcription initiation defects caused by promoter insertions of the transposable element Ty.