SII-SWORD/CoKE huggingface dataset:
Pfam PF18065: PatG C-terminal (domain)
This is the C-terminal domain of Prochloron sp. PatG, which process the precursor peptide to yield the cyclic Patellamide. The C-terminal domain of PatG is 56% structurally homologous to the C-terminal domain of PatA.
Pfam PF18608: XIAP-associated factor 1 C-terminal domain (domain)
XIAP-associated factor 1 (XAF1) is a 301-amino acids interferon (INF)-inducible pro-apoptotic protein. The XIAP binding region within XAF1, XIAP RING binding site, is located at the C-terminal portion of XAF1. This entry represents the C-terminal region which is functionally identified as XIAP RING-binding domain of XAF1.
Pfam PF18993: Rv0078B-related antitoxin (family)
Putative antitoxin protein according to TASmania database.
Pfam PF20944: Metalloprotease StcE, beta-sandwich domain (domain)
This domain is found in Metalloprotease StcE from Escherichia coli and similar proteins predominantly found in Gammaproteobacteria. StcE is a virulence factor that contributes to intimate adherence to host cells. This enzyme is organised into three distinct globular domains, IG, M and C, that are packed against each other to show an overall T-shape. This entry represents a region that is located within the domain IG. This region folds independently as a mixed, eight-stranded beta-sandwich and contains an additional beta-strand followed by a perpendicular arrangement of two alpha-helices in its N terminus. It is also known as the INS domain. This entry also covers a disordered region that has been described as D1.
Pfam PF10322: Serpentine type 7TM GPCR chemoreceptor Sru (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Sru is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF04381: Putative exonuclease, RdgC (family)
Members of the RdgC family may have exonuclease activity. RdgC is required for efficient pilin variation in Neisseria gonorrhoeae, suggesting that it may be involved in recombination reactions. In Escherichia coli, RdgC is required for growth in recombination-deficient exonuclease-depleted strains.  Under these conditions, RdgC may act as an exonuclease to remove collapsed replication forks, in the absence of the normal repair mechanisms.
Pfam PF04437: RINT-1/TIP-1 family (repeat)
This family includes TIP-1 (also known as Tip20) protein from yeast which is part of the  Dsl1 complex, a multisubunit tethering complex involved in retrograde trafficking of vesicles from Golgi to ER, its homologue from animals RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control and in membrane trafficking from the endoplasmic reticulum (ER) to the Golgi complex; and MAIGO2 (Mag2) from plants which functions in the transport of storage protein precursors between the ER and Golgi complex. They are part of the CATCHR (complexes associated with tethering containing helical rods) family which includes proteins from the GARP/EARP, exocyst, conserved oligomeric Golgi (COG), and Dsl1 complexes and share a structural fold consisting of helical bundles.
Pfam PF00581: Rhodanese-like domain (domain)
Rhodanese has an internal duplication.  This Pfam represents a single copy of this duplicated domain.  The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.
Wikipedia: Rhodanese is a mitochondrial enzyme that detoxifies cyanide (CN−) by converting it to thiocyanate. In enzymatology, the common name is listed as thiosulfate sulfurtransferase. The diagram on the right shows the crystallographically-determined structure of rhodanese.
Pfam PF25015: AKAP-17A-like, RNA-binding domain (domain)
This domain is found in human A-kinase anchor protein 17A (AKAP-17A), a splice factor regulating alternative splice site selection for certain mRNA precursors. This domain is predicted to show an alpha-beta configuration.
Pfam PF13435: Cytochrome c554 and c-prime (family)
This family is a tetra-haem cytochrome involved in the oxidation of ammonia. It is found in both phototrophic and denitrifying bacteria.
Pfam PF14431: YwqJ-like deaminase (family)
A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Bacillus YwqJ. Members of this family are present in a wide phyletic range of bacteria and a few basidiomycetes. Bacterial versions are predicted to function as toxins in bacterial  polymorphic toxin systems.
Pfam PF17517: IgGFc binding protein (family)
This domain is found at the N terminal of [swissprot:Q9Y6R7] and has been shown to confer IgG Fc binding activity. It may play a role in immune protection and inflammation in the intestines of primates.
Pfam PF11618: First C2 domain of RPGR-interacting protein 1 (domain)
This domain is the first, more N-terminal, C2 domain on X-linked retinitis pigmentosa GTPase regulator-interacting proteins, or RPGR-interacting proteins.
Pfam PF11487: Type II restriction enzyme SfiI (family)
SfiI is a restriction enzyme that can cleave two DNA sites simultaneously to leave 3-base 3' overhangs. It acts as a homo-tetramer and recognises a specific eight base-paid palindromic DNA sequence. After binding two copies of its recognition sequence, SfiI becomes activated leading to cleavage of all four DNA strands. The structure of SfiI consists of a central twisted beta-sheet surrounded by alpha-helices.
Pfam PF15114: Uncharacterised protein family UPF0640 (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 80 amino acids in length. There are two conserved sequence motifs: PGK and YRFLP.
Pfam PF01411: tRNA synthetases class II (A) (family)
Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases.
Pfam PF18888: Repeat of unknown function (DUF5650) (repeat)
This entry represents a repeating region found in filamentous hemagglutinin proteins from various bacteria. This entry may contain a beta helix structure.
Pfam PF19118: Family of unknown function (DUF5802) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF22022: Phage integrase central domain (domain)
This is the central domain of phage integrases. This domain is known to mediate DNA binding and binds to the major groove adjacent to the site of DNA cleavage. It consists of two pairs of antiparallel helices that pack together at nearly a right angle and form a four-helix bundle.
Pfam PF09579: Sporulation protein YtfJ (Spore_YtfJ) (family)
Proteins in this family are encoded by bacterial genomes if, and only if, the species is capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF.
Pfam PF17984: Telomerase reverse transcriptase thumb DNA binding domain (domain)
The catalytic subunit of telomerase is structurally similar to retroviral reverse transcriptases, viral RNA polymerases and, to a lesser extent, the bacteriophage B-family DNA polymerases. Like its structural homologs, the core catalytic subunit of telomerase, TERT, contains the fingers, palm and thumb domains required for nucleic acid and nucleotide associations as well as catalysis. The four major TERT domains: the RNA binding domain (TRBD); the fingers domain, implicated in nucleotide binding and processivity; the palm domain, which contains the active site of the enzyme; and the thumb domain, implicated in DNA binding and processivity are organized into a ring configuration similar to that observed for the substrate-free enzyme. This is the thumb domain found in Tribolium castaneum telomerase catalytic subunit, TERT. Contacts between TERT and the DNA substrate are mostly mediated via backbone interactions with the thumb loop and helix. The thumb helix sits in the minor groove of the RNA-DNA heteroduplex, making extensive contacts with the phosphodiester backbone and the ribose groups of the RNA-DNA hybrid.
Pfam PF12562: Poxvirus telomere-binding protein I6, C-terminal domain (domain)
This domain is found at the C-terminal end of Telomere-binding protein I6 from poxvirus, I6 binds tightly and with great specificity to the hairpin form of the viral telomeric sequence. This protein is thought to play a role in the initiation of vaccinia virus genome replication and/or genome encapsidation. The family is found in association with [pfam:PF04595].
Pfam PF05977: Transmembrane secretion effector (family)
This is a family of transport proteins. Members of this family include a protein responsible for the secretion of the ferric chelator, enterobactin, and a protein involved in antibiotic resistance.
Pfam PF04080: Per1-like family (family)
PER1 is required for GPI-phospholipase A2 activity and is involved in lipid remodelling of GPI-anchored proteins. PER1 is part of the CREST superfamily.
Pfam PF03634: TCP family transcription factor (family)
This is a family of TCP plant transcription factors.  TCP proteins were named after the first characterised members (TB1, CYC and PCFs) and they are involved in multiple developmental control pathways.  This region contains a DNA binding basic-Helix-Loop-Helix (bHLP) structure.
Wikipedia: In molecular biology, the protein domain TCP is actually a family of transcription factors named after: teosinte branched 1, cycloidea (cyc) and PCF in rice.
Pfam PF12770: CHAT domain (domain)
These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins.
Pfam PF23505: YqgG (family)
This protein family includes Protein YqgG from Escherichia coli, a 47-residues micropeptide encoded by a small open reading frame (smORF) found antisense to yqgC. Proteins 50 or fewer residues -long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF04335: VirB8 protein (domain)
VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the NTF2 protein.
Pfam PF13880: ESCO1/2 acetyl-transferase (domain)
This entry represents the acetyl-transferase domain of the acetyl-transferase ESCO. N-acetyltransferase ESCO1 and ESCO2 are required for the establishment of sister chromatid cohesion and couple the processes of cohesion and DNA replication to ensure that only sister chromatids become paired together. They act by mediating the acetylation of cohesin component SMC3 . They feature a conserved C-terminal domain consisting of a H2C2 zinc finger motif (IPR028005) and an acetyltransferase domain, while the diverse N-terminal domain is involved in chromosome binding and could target these proteins to different chromosome structures .
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF08012: Protein of unknown function (DUF1702) (family)
This family of proteins contains many bacterial proteins that are encoded by the UnbL gene.           The function of these proteins is 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 PF15274: Muscular LMNA-interacting protein (family)
MLIP is a Muscle-enriched A-type Lamin-interacting Protein, an innovation of amniotes, and is expressed ubiquitously and most abundantly in heart, skeletal, and smooth muscle. MLIP interacts directly and co-localises with lamin A and C in the nuclear envelope. MLIP also co-localises with promyelocytic leukemia (PML) bodies within the nucleus. PML, like MLIP, is only found in amniotes, suggesting that a functional link between the nuclear envelope and PML bodies may exist through MLIP.
Pfam PF24143: EGF-like domain-containing protein ComC second beta-sandwich (domain)
This entry represents the second beta-sandwich domain found in EGF-like domain containing protein ComC from amoebas. This protein regulates aggregation, inhibiting lagC and activating lagD expression. The function of this domain is unknown.
Pfam PF16634: Unstructured region on APC between APC_crr and SAMP (disordered)
APC_u13 is a short region of natively unstructured sequence lying between the fourth creatine-rich region, APC_crr, [pfam:PF05923], and the SAMP [pfam:PF05924], domains on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known.
Pfam PF02607: B12 binding domain (domain)
This B12 binding domain is found in methionine synthase [ec:2.1.1.13] [swissprot:Q99707], and other shorter proteins that bind to B12. This domain is always found to the N-terminus of [pfam:PF02310]. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.
Wikipedia: In molecular biology, the vitamin B12-binding domain is a protein domain which binds to cobalamin. It can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain. Proteins containing the cobalamin-binding domain include:Animal and prokaryotic methionine synthase, which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine.
Animal and prokaryotic methylmalonyl-CoA mutase, which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle.
Prokaryotic lysine 5,6-aminomutase.
Prokaryotic glutamate mutase.
Prokaryotic methyleneglutarate mutase.
Prokaryotic isobutyryl-CoA mutase.
Pfam PF05087: Rotavirus VP2 protein (family)
Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3.
Pfam PF25124: Domain of unknown function (DUF7816) (domain)
This domain is found towards the C terminus of human NEDD4 -binding protein 2 (N4BP2), which has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination. This domain is predicted to adopt an alpha configuration. Its specific function is unknown. It is normally found N-terminal to [pfam:PF08590].
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 PF17961: Bacterial Ig domain (domain)
This entry represents a bacterial Ig-fold domain that is found in  a wide range of bacterial cell surface adherence proteins.
Pfam PF08712: Scaffold protein Nfu/NifU N terminal (domain)
This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein.  Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters.
Pfam PF02026: RyR domain (family)
This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
Wikipedia: The ryanodine-inositol 1,4,5-triphosphate receptor Ca2+ channel (RIR-CaC) family includes Ryanodine receptors and Inositol trisphosphate receptors. Members of this family are large proteins, some exceeding 5000 amino acyl residues in length. This family belongs to the Voltage-gated ion channel (VIC) superfamily. Ry receptors occur primarily in muscle cell sarcoplasmic reticular (SR) membranes, and IP3 receptors occur primarily in brain cell endoplasmic reticular (ER) membranes where they effect release of Ca2+ into the cytoplasm upon activation (opening) of the channel. They are redox sensors, possibly providing a partial explanation for how they control cytoplasmic Ca2+. Ry receptors have been identified in heart mitochondria where they provide the main pathway for Ca2+ entry. Sun et al. (2011) have demonstrated oxygen-coupled redox regulation of the skeletal muscle ryanodine receptor-Ca2+ release channel (RyR1;TC# 1.A.3.1.2) by NADPH oxidase 4.
Pfam PF22274: DGF-1 beta-sheet domain (repeat)
This entry represents a beta-sheet domain present in DGF-1 from Typanosoma proteins, one of the most abundant proteins in T. cruzi genome. This domain adopts a pectin lyase-like fold. The function of this protein is not yet clear, however, it is likely to play a role in cell-to-cell interactions or signal transduction.
Pfam PF06256: Nucleopolyhedrovirus LEF-12 protein (family)
This family consists of several Nucleopolyhedrovirus late expression factor-12 (LEF-12) proteins. The function of this family is unknown.
Pfam PF20163: Family of unknown function (DUF6536) (family)
Proteins in this family are found in Fungi.
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 PF23713: Egalitarian winged helix domain (domain)
This entry represents a winged-helix domain found in the C. elegans protein egalitarian. The Egalitarian (Egl) protein functions as part of a complex with BicaudalD (BicD) and dynein light chain (DLC-1) to recruit the dynein motor complex to specific cargoes and regulate dynein activity. In C. elegans, the EGAL-1 protein (homolog of Egalitarian) interacts with both the BICD-1 and DLC-1 proteins. Genetic disruption of egal-1 leads to defects in hyp7 nuclear migration, similar to defects seen when disrupting bicd-1 or components of dynein. The egal-1 phenotype is enhanced when combined with a nud-2 mutant, but not enhanced by bicd-1, suggesting egal-1 and bicd-1 function in the same genetic pathway. A model is proposed where BICD-1, EGAL-1 and DLC-1 form a complex that is recruited by the nuclear envelope protein UNC-83. This complex then helps recruit the dynein motor to the nuclear envelope to regulate nuclear migration.
Pfam PF05135: Phage gp6-like head-tail connector protein (domain)
This family of proteins contain head-tail connector proteins related to gp6 from bacteriophage HK97. A structure of this protein shows similarity to gp15 a well characterised connector component of bacteriophage SPP1.
Pfam PF13372: Alginate export (domain)
This domain forms an 18-stranded beta-barrel pore which is likely to act as an alginate export channel.
Pfam PF01141: Gag polyprotein, inner coat protein p12 (family)
The retroviral p12 is a virion structural protein. p12 is proline rich.  The function carried out by p12 in assembly and replication is unknown.  p12 is associated with pathogenicity of the virus.
Pfam PF11008: Protein of unknown function (DUF2846) (family)
Some members in this family of proteins with unknown function are annotated as lipoproteins however this cannot be confirmed.
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 PF18863: AbiJ N-terminal domain 4 (domain)
Alpha + beta. Found fused to AbiJ-like HEPN and heat repeats.
Pfam PF06803: Protein of unknown function (DUF1232) (family)
This family represents a conserved region of approximately 60 residues within a number of hypothetical bacterial and archaeal proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF20508: Family of unknown function (DUF6734) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 430 and 555 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.