SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF3262 (DUF3262)
Type: Family

This entry represents small, hydrophobic proteins that are found occasionally on plasmids such as the Pseudomonas putida TOL (toluene catabolic) plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Protein of unknown function DUF2986 (DUF2986)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF3263 (DUF3263)
Type: Family

This family of proteins with unknown function appears to be restricted to Actinobacteria.
Toxin endonuclease, YhaV (Toxin_endonuclease_YhaV)
Type: Family

YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF. The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity .
Protein of unknown function DUF2933 (DUF2933)
Type: Family

This bacterial family of proteins has no known function.
Putative zincin peptidase (DUF3267)
Type: Family

This family of proteins has a conserved HEXXH motif, suggesting the members are putative peptidases of zincin fold .
WW domain-binding protein 1-like (WBP1-like)
Type: Family

This entry includes WBP-1 and its homologous. WBP-1 is a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain . This entry also includes transmembrane protein 92 (TMEM92), whose function is not clear.
Major surface protein 1a (MSP1a) (MSP1a)
Type: Family

MSP1a is part of the A.marginale major surface protein 1 (MSP1) complex and exists as a heterodimer with MSP1b. The complex has adhesive functions in bovine erythrocytes invasion .
Protein of unkown function DUF3268 (DUF3268)
Type: Family

This is a family of bacterial and plasmid sequences that carry at least one zinc-finger towards the N terminus and a possible second at the C terminus.
Protein of unknown function DUF3269 (DUF3269)
Type: Family

This entry includes Bacteriophage 92, Orf70. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF3270 (DUF3270)
Type: Family

This family of proteins with unknown function appears to be restricted to Streptococcus.
Protein of unknown function DUF3271 (DUF3271)
Type: Family

This family of proteins with unknown function appears to be restricted to Plasmodium.
Protein of unknown function DUF3272 (DUF3272)
Type: Family

This family of proteins with unknown function appears to be restricted to Streptococcus.
Protein of unknown function DUF3273 (DUF3273)
Type: Family

Some members in this family of proteins are annotated as multi-transmembrane proteins however this cannot be confirmed. Currently this family has no known function.
Antibacterial effector protein Tle3, C-terminal (Tle3_C)
Type: Domain

This entry represents the C-terminal domain of Antibacterial effector protein Tle3 from Pseudomonas aeruginosa and similar sequences from proteobacteria. Tle3 is toxic once delivered in the periplasm of prey bacteria .
Protein of unknown function DUF3275 (DUF3275)
Type: Family

This family of proteins with unknown function appear to be restricted to Proteobacteria.
Structural protein ORF10, bacteriophage KPP10 (Phage_KPP10_Orf10)
Type: Family

This entry is represented by Bacteriophage KPP10 Structural protein ORF10, whose function is unknown. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Domain of unknown function DUF3279 (DUF3279)
Type: Domain

This domain is found in uncharacterised proteins with unknown function and appears to be restricted to Enterobacteriaceae. It is predicted to adopt a structure typical for zinc-ribbon domains.
Protein of unknown function DUF3278 (DUF3278)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF2380 (DUF3280)
Type: Family

This family of proteins with unknown function appears to be restricted to Proteobacteria.
Protein of unknown function DUF3281 (DUF3281)
Type: Family

This family of bacterial proteins has no known function. This entry includes bacterial lipoprotein FTN_103 from Francisella novicida .
Protein of unknown function DUF3283 (DUF3283)
Type: Family

This family of proteins with unknown function appears to be restricted to Proteobacteria.
Protein of unknown function DUF3284 (DUF3284)
Type: Family

This family of proteins with unknown function appears to occur predominantly in Firmicutes.
Protein of unknown function DUF3285 (DUF3285)
Type: Family

This family of proteins with unknown function are mostly from Cyanobacteria.
Protein of unknown function DUF3287 (DUF3287)
Type: Family

This eukaryotic family of proteins has no known function.
Protein of unknown function DUF3288 (DUF3288)
Type: Family

This family of proteins with unknown function are mostly from Cyanobacteria.
Protein of unknown function DUF2990 (DUF2990)
Type: Family

This family of proteins represents a fungal protein with unknown function.
Protein of unknown function DUF3290 (DUF3290)
Type: Family

This family of bacterial proteins is functionally uncharacterised.
Domain of unknown function DUF3291 (DUF3291)
Type: Domain

This bacterial family of proteins has no known function.
Protein of unknown function DUF3292 (DUF3292)
Type: Family

This eukaryotic family of proteins has no known function.
Protein of unknown function DUF3293 (DUF3293)
Type: Family

This bacterial family of proteins has no known function.
Domain of unknown function DUF3295 (DUF3295)
Type: Domain

This is a conserved region found in fungi, whose function is unknown. They contain a GATA-like domain at the N-terminal (

).
Uncharacterised domain UPF0506 (UPF0506)
Type: Domain

This uncharacterised family is found mainly in Schistosoma genomes. Although uncharacterised it appears to belong to the knottin fold. The sequence is composed of two repeats of a 6 cysteine motif.
Folliculin (Folliculin)
Type: Family

In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex . Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterised by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases .
Nucleolar pre-ribosomal-associated protein 1, N-terminal (Npa1_N)
Type: Domain

Nucleolar pre-ribosomal-associated protein 1 (Npa1) is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits . The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre . The protein has also been referred to as Urb1.

This entry represents a domain is found at the N terminus of Npa1.
Pre-mRNA-splicing factor SLU7 domain (Slu7_dom)
Type: Domain

The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions . Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3' splice site from targeted RNase H cleavage. This change, which probably reflects binding of the 3' splice site PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain; this retains the protein within the nucleus .
Thrombin inhibitor Madanin (Inhibitor_I53)
Type: Domain

Members of this family are the peptidase inhibitor madanin proteins. These proteins were isolated from tick saliva .
Nucleoporin Nup120/160 (Nucleoporin_Nup160)
Type: Family

Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth . The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export . Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 subcomplex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 subcomplex, but rather that it regulates the association of the subcomplex with the NPC and other proteins .
Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term (CPSF73-100_C)
Type: Domain

This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.
Proteinase inhibitor I78 (Prot_inh_I78)
Type: Family

This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78 .
Malectin domain (Malectin_dom)
Type: Domain

Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186. NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated "malectin", and its endogenous ligand is found to be Glc2-high-mannose N-glycan .

This entry represents a malectin domain, and can also be found in probable receptor-like serine/threonine-protein kinases from plants and in proteins described as glycoside hydrolases.
Zinc finger, CCCH-type, TRM13 (Znf_CCCH-type_TRM13)
Type: Domain

This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.
YvbH-like, oligomerisation domain (YvbH_oligomer_dom)
Type: Domain

This domain is found at the C terminus of a group of bacterial uncharacterised proteins. This domain is composed of a helical hairpin that appears to mediate oligomerization based on the known structure .
Protein of unknown function DUF3297 (DUF3297)
Type: Family

This family is expressed in Proteobacteria and Actinobacteria. The function is not known.
Pathogenicity locus (Cdd1)
Type: Family

Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria . Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
THO complex, subunitTHOC2, N-terminal (THO_THOC2_N)
Type: Domain

The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats . In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex .

This entry represents a conserved domain found towards the N terminus of these proteins.
Protein of unknown function DUF3299 (DUF3299)
Type: Family

This is a family of bacterial proteins of unknown function.
Protein of unknown function DUF3300 (DUF3300)
Type: Family

This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
Domain of unknown function DUF3298 (DUF3298)
Type: Domain

This entry represents a highly conserved domain found in a group of bacterial proteins. The function of this domain is not known. Proteins containing this domain include pdaC and anti-sigma-V factor RsiV from Bacillus subtilis. PdaC catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme .
YdbH-like (YdbH)
Type: Family

This protein family includes the probable phospholipid transport protein YdbH protein from E.coli and similar proteins mainly found in proteobacteria. YdbH is one of the six AsmA-like paralogues in E.coli (YhdP, TamB, YdbH, AsmA, YicH, and YhjG) that have a variable size but share a similar predicted structure. In-depth functional characterisation of AsmA-like proteins revealed that YdbH together with the other largest paralogs (YhdP and TamB) are redundant in performing a function that is essential for growth and OM lipid homeostasis in E.coli . The current model based on these analyses suggests that TamA-TamB, YhdP, and YdbH form bridge-like structures that mediate the diffusional flow of phospholipids between the IM and OM .
AMIN domain (AMIN_dom)
Type: Domain

This N-terminal domain of various bacterial protein families is crucial for the targetting of periplasmic or extracellular proteins to specific regions of the bacterial envelope. AMIN is derived from the N-terminal domain of AmiC, an N-acetylmuramoyl-l-alanine amidase of Escherichia coli which localises to the septal ring during division and plays a key role in the separation of daughter cells. The AMIN domain is present in several protein families besides amidases suggesting that AMIN may represent a general targetting determinant involved in the localisation of periplasmic protein complexes .
Protein of unknown function DUF3301 (DUF3301)
Type: Family

This family is conserved in Proteobacteria, but the function is not known.
Protein of unknown function DUF3304 (DUF3304)
Type: Family

This is a family of bacterial proteins of unknown function.
Protein of unknown function DUF3303 (DUF3303)
Type: Family

Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
Protein of unknown function DUF3306 (DUF3306)
Type: Family

This family of proteobacterial species proteins has no known function.
Protein of unknown function DUF3305 (DUF3305)
Type: Family

Several members of this family are annotated as being molybdopterin-guanine dinucleotide biosynthesis protein A; however, this could not be confirmed. The family is found in proteobacteria.
Bacteriophage phiKZ, Orf197 (Phage_phiKZ_Orf197)
Type: Family

This entry is represented by Bacteriophage phiKZ, Orf197. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF3309 (DUF3309)
Type: Family

This family is conserved in bacteria but its function is not known.
SaV-like (SaV-like)
Type: Family

This entry includes bacteriophage T7, Gp1.7, which is a nucleotide kinase that catalyzes the phosphorylation of dGMP and dTMP to dGDP and dTDP . It also includes SaV from Lactococcus phage p2, which is involved in sensitivity to the host abortive infection mechanism AbiV . The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Velvet factor (Velvet)
Type: Family

The velvet factor is conserved in many fungal species and is found to have gained different roles depending on the organism's need, expanding the conserved role in developmental programmes . The velvet factor orthologues can be adapted to the fungal-specific life cycle and may be involved in diverse functions such as sclerotia formation and toxin production, as in Aspergillus parasiticus , nutrition-dependent sporulation, as in A. fumigatus , or the microconidia-to-macroconidia ratio and cell wall formation, as in the heterothallic fungus Gibberella moniliformis (Fusarium verticillioides).
Protein of unknown function DUF3311 (DUF3311)
Type: Family

This is a family of short bacterial proteins of unknwon function.
Suppressor of RNA silencing P21-like, N-terminal (RSS_P20_N)
Type: Domain

This entry represent a domain found in a group of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted α-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly α-helical secondary structure in the P21-like proteins .
Keratin-associated protein, type8/19/20/21/22 (KRTAP_type8/19/20/21/22)
Type: Family

The major structural proteins of mammalian hair are the hair keratin intermediate filaments (KIFs) and the keratin-associated proteins (KRTAPs). In the hair cortex, hair keratins are embedded in an inter-filamentous matrix consisting of KRTAPs which are essential for the formation of a rigid and resistant hair shaft as a result of disulphide bonds between cysteine residues. There are essentially three groups of KRTAPs, viz: the high-sulphur (HS) and ultra-high-sulphur (UHS) KRTAPs (cysteine content: 16-30 and >30 mol%, respectively) and the high-glycine/tyrosine (HGT: 35-60 mol% glycine and tyrosine) KRTAPs.
Cobalamin synthesis G, N-terminal (CbiG_N)
Type: Domain

Members of this family are involved in cobalamin synthesis. The gene encoded by

has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process . Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B. The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear.
Cobalamin biosynthesis central region (CbiG_mid)
Type: Domain

Members of this family are involved in cobalamin synthesis. The gene encoded by

has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process .
DIPSY domain (DIPSY)
Type: Domain

The DIPSY domain is characterised by the distinctive D*I*PSY motif at the very C terminus of yeast cell-wall glycoproteins. It appears not to be conserved in any other species, however. In fungi, cell adhesion is required for flocculation, mating and virulence, and is mediated by covalently bound cell wall proteins termed adhesins. Map4, an adhesin required for mating in Schizosaccharomyces pombe, is N-glycosylated and O-glycosylated, and is an endogenous substrate for the mannosyl transferase Oma4p. Map4 has a modular structure with an N-terminal signal peptide, a serine and threonine (S/T)-rich domain that includes nine repeats of 36 amino acids (rich in serine and threonine residues, but lacking glutamines), and a C-terminal DIPSY domain with no glycosyl-phosphatidyl inositol (GPI)-anchor signal. The N-terminal S/T-rich regions, are required for cell wall attachment, but the C-terminal DIPSY domain is required for agglutination and mating in liquid and solid media .
Protein of unknown function DUF3313 (DUF3313)
Type: Family

This a bacterial family of proteins which are annotated as putative lipoproteins.
Protein of unknown function DUF3314 (DUF3314)
Type: Family

This small family contains human, mouse and fish members but the function is not known.
Competence protein ComGE (ComGE)
Type: Family

This entry includes the competence protein ComGE (protein E of the comG locus), found in multiple species of Streptococcus. It is required for formation of the type IV-like pilus (T4P) that plays a role in transformation .
Septation initiation Sid4-like (Sid4-like)
Type: Family

This entry includes fission yeast Sid4 and its homologue, Ady3 and Cnm67, from budding yeasts.
Protein of unknown function DUF3318 (DUF3318)
Type: Family

This is a bacterial family of uncharacterised proteins.
Transcription initiation factor Rrn7, Zinc-finger (TF_Rrn7_Zf)
Type: Domain

This entry represents the zinc-finger found in the N terminus of the Rrn7 protein. Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter .
Protein of unknown function DUF3319 (DUF3319)
Type: Family

This is a family of short bacterial proteins, a few of which are annotated as being minor tail protein. Otherwise the function is unknown.
Domain of unknown function DUF3320 (DUF3320)
Type: Domain

This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Transcription factor Aft1, HRA domain (TF_Aft1_HRA)
Type: Domain

This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRA domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to activate recombination .
Transcription factor Aft1, HRR domain (TF_Aft1_HRR)
Type: Domain

This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRR domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to repress recombination .