SII-SWORD/CoKE huggingface dataset:
Anti-sigma factor RsgI, N-terminal (Anti-sigma_RsgI_N)
Type: Domain

The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation , and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes . Regulation of sigma factor I is carried out by RsgI from the same operon.

This entry represents the N-terminal anti-sigma domain, which is located in cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I .
Domain of unknown function DUF3874 (DUF3874)
Type: Domain

This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
TraG, N-terminal, Bacteroidetes (TraG_N_Bacteroidetes)
Type: Domain

This domain of unknown function is found in proteins from Bacteroidetes, including the conjugation system ATPase, TraG.
Protein of unknown function DUF3876 (DUF3876)
Type: Family

This bacterial family of conserved proteins has no known function.
Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family (Peptidase_C92)
Type: Family

Amidase_YiiX is a family of permuted papain-like amidases. It has amidase specificity for the amide bond between a lipid and an amino acid (or peptide). From the structure, a tetramer, each monomer is made up of a layered α-β fold with a central, 6-stranded, antiparallel β-sheet that is protected by helices on either side. The catalytic Cys154 in

,

, is located on the N terminus of helix αF. The two additional helices located above Cys154 contribute to the formation of the active site, where the lysine ligand is bound .

This family also includes poxvirus protein G6 (also known as OPG091) which has sequence similarity with a group of bacterial permuted papain-like amidases, whose gene might have been acquired from a bacterial source at the onset of poxvirus evolution .
Phage capsid (Phage_capsid)
Type: Family

The proteins in this family are found in bacteria and viruses (Caudovirales) and represent bacteriophage capsid proteins. The major capsid protein of Enterobacteria phage HK97 assembles to form an icosahedral capsid . Included within the capsid protein is the delta domain which acts as the scaffold upon which the capsid is built . Bacterial and archaeal encapsulin-like systems and HK97-type viruses share a common ancestor and it is likely that encapsulins have evolved from HK97-type phages

].
Integrase catalytic domain, putative (Integrase_catalytic_putative)
Type: Domain

Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment .

This entry represents the catalytic domain from a family of putative prophage DNA-binding integrases.
Putative integrase, N-terminal (Putative_integrase_N)
Type: Domain

Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment .

This entry represents the N-terminal predicted α-helical domain found in a family of putative prophage DNA-binding integrases.
Anti-CBASS protein Acb1-like, N-terminal domain (Acb1-like_N)
Type: Domain

This domain is found at the N-terminal end of Anti-CBASS protein Acb1 from Sphingomonas paeninsulae and similar sequences from tailed bacteriophages and bacterial prophages. Abc1 counteracts or regulates the endogenous CBASS (cyclic oligonucleotide-based antiphage signalling system) antiviral defence system. It is a phosphodiesterase that enables metal-independent hydrolysis of the host cyclic di- and trinucleotide CBASS signals such as 3'3'-cGAMP, 3'3'cUA, and 3'3'3'-cAAA . This domain is also found covering the whole length of the protein in many uncharacterised sequences.
Protamine-like (Protamine-like)
Type: Family

This entry represent a group of insect proteins, including protamine A (ProtA), protamine B (ProtB) and protamine-like protein 99C (Prtl99C) from Drosophila melanogaster. They contain a HMG-box and are involved in chromatin compaction during spermiogenesis . Prtl99C is a sperm chromatin-associated protein that is essential for male fertility .
Coiled-coil domain-containing protein 90-like (CCDC90-like)
Type: Family

This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1 . A study in mammals and in yeast homologue fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU , however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU . The role of CCDC90B proteins is still not known.
Glycosyl-hydrolase family 116, N-terminal (GH116_N)
Type: Domain

This entry represents the N-terminal domain found in the CAZyme GH116 family members, which presently includes enzymes with beta-glucosidase (

), beta-xylosidase (

) , and glucocerebrosidase (

) activity . The N-terminal is thought to be the luminal domain while the C-terminal is the cytosolic domain.

Proteins containing this domain include animal non-lysosomal glucosylceramidase GBA2, which catalyse the conversion of glucosylceramide to free glucose and ceramide . GBA2 is involved in sphingomyelin generation and prevention of glycolipid accumulation and may also catalyse the hydrolysis of bile acid 3-O-glucosides, however, the relevance of such activity is unclear in vivo . Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia .
Transposase TnpC, homeodomain (Transposase_TnpC_homeodom)
Type: Domain

This entry represents a leucine-zipper-like, or homeodomain-like, region of the transposase TnpC from insertion element IS66 .
Protein of unknown function DUF2391 (DUF2391)
Type: Family

Members of this protein family are found in archaea and bacteria. Their function is unknown.
Domain of unknown function DUF2399 (DUF2399)
Type: Domain

This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Conserved hypothetical protein CHP02679, N terminus (CHP02679_N)
Type: Domain

This domain is found to the N terminus of bacterial conserved hypothetical proteins which are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria).
Antitoxin Xre/MbcA/ParS-like, toxin-binding domain (Xre/MbcA/ParS-like_toxin-bd)
Type: Domain

This entry represents the C-terminal domain of antitoxin components of a type II toxin-antitoxin (TA) system, including Xre from Pseudomonas putida, MbcA from Mycobacterium sp. and ParS from Sphingobium sp. . This domain interacts with the toxin component (RES, MbcT and ParT respectively) and sterically blocks its active site, neutralizing its effect .
Sec16, N-terminal (Sec16_N)
Type: Domain

Sec16 is a multi-domain vesicle coat protein. The overall function of Sec16 is in mediating the movement of protein-cargo between the organelles of the secretory pathway. The yeast protein Sec16 plays a key role in the formation of coat protein II vesicles, which mediate protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus .

This entry represents the N terminus of the Sec16 protein found in fungi. Over-expression of truncated mutants of only the N terminus are lethal, and this portion does not appear to be essential for function so may act as a stabilising region .
Protein of unknown function DUF2538 (DUF2538)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF2545 (DUF2545)
Type: Family

This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. Their sequences are highly conserved.
Protein of unknown function DUF2715 (DUF2715)
Type: Family

This family of proteins with unknown function appears to be largely found in spirochaete bacteria. They are related to membrane β barrel proteins.
Transposase, IS4, N-terminal (Transposases_IS4_N)
Type: Domain

This entry represents the N-terminal domain of Insertion Element 4 transposases .
Transposase IS66, zinc-finger binding domain of (Znf_dom_IS66)
Type: Domain

This is a zinc-finger region of the N terminus of the insertion element IS66 transposase .
Type IV conjugative transfer protein TrbJ/K, C-terminal (TrbJ/K_C)
Type: Domain

This domain is found C-terminal in bacterial proteins encoded by the TrbJ and TrbK genes of the Ti plasmid conjugative transfer operon .
Protein of unknown function DUF3861 (DUF3861)
Type: Family

This entry represents a family of proteins of unknown function which are found predominantly in the proteobacteria. The structurally characterised member of this family (

) adopts a novel fold consisting of a long N-terminal β-hairpin followed by three α helices. This structure shows some resemblance to three-helical bundle folds such as the serum albumin-like fold.
Protein of unknown function DUF3865, CADD-like (DUF3865_CADD-like)
Type: Family

This entry represents a family of proteins of unknown function. The Nostoc punctiforme protein (

) has been structurally characterised and adopts a heme oxygenase-like fold similar to that of the Chlamydia trachomatis death domain-binding CADD protein. The proposed active sites of the Nostoc and Chlamydia sequences are identical, suggesting similar functions.
Chemotaxis methyl-accepting receptor HlyB-like, 4HB MCP domain (HlyB_4HB_MCP)
Type: Domain

This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors .

This domain is found in a group of methyl-accepting chemotaxis receptors that includes Vibrio cholerae HlyB .
Protein of unknown function DUF3866 (DUF3866)
Type: Family

This family of proteins is currently functionally uncharacterised.
Domain of unknown function DUF3868 (DUF3868)
Type: Domain

This domain of unknown function is found at the N-terminal end of a group of proteins from bacteroidetes. The function of the proteins is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture .
Helicase Sen1, N-terminal (Helicase_Sen1_N)
Type: Domain

The yeast helicase Sen1 is an ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs and it also has an ATPase-dependent ability of promoting transcription termination in vitro . Sen1 has a key role at replication forks during DNA replication to promote fork progression and chromosome stability . Sen1 belongs to the superfamily 1B UPF1-like family of helicases with a common domain organisation: a N-terminal domain and a C-terminal domain which contains the SF1B RNA helicase with two RecA domains (RecA1 and RecA2) and the classical helicase motifs involved in nucleic acid binding and ATP hydrolysis. It also contains two SF1B-specific subdomains (1B and 1C) that modulate RNA binding. This entry represents the large N-terminal domain, a characteristic feature of this protein, which is important for Sen1 function in vivo. It is sufficient and necessary for replisome association as it contains the interaction sites for replisome components .
Domain of unknown function DUF3855 (DUF3855)
Type: Domain

This domain forms an unusual α/β fold where a six-stranded antiparallel β-sheet is wrapped around a central α-helix, flanked by an additional α-helix and a small sub-domain consisting of a single β-strand and a two-stranded antiparallel β-sheet . It shows weak structural similarities to phosphoribosylformylglycinamidine synthases and some thioesterase superfamily members, but its function is unknown.
Glia associated membrane protein glam-1 (Glam1)
Type: Family

This entry represents Glia associated membrane protein glam-1 from Caenorhabditis elegans (Glam1) and similar worm proteins.
Protein of unknown function DUF2709 (DUF2709)
Type: Family

Members of this family appear restricted to Chlamydiales. Their function is unknown.
Protein of unknown function DUF2680 (DUF2680)
Type: Family

Members in this family of proteins are annotated as YckD however currently no function is known.
Protein of unknown function DUF2617 (DUF2617)
Type: Family

This is a family of proteins with unknown function.
Cellulose biosynthesis protein BcsR-like (CBP_BcsR)
Type: Family

Cellulose is necessary for biofilm formation in bacteria and is synthesized by the bacterial cellulose biosynthesis complex (Bcs) which is widespread among beta and gamma proteobacteria . CBP_BcsR is a small subunit of this complex, essential for cellulose secretion . It may play a regulatory role together with BcsQ subunit as they form a subcomplex with chaperone-like function toward each other . BcsR stabilizes BcsQ to form monodisperse BcsR2Q2 heterotetramers in solution and BcsQ may play a role in the folding and subsequent stability of BcsR .
Protein of unknown function DUF2777 (DUF2777)
Type: Family

This family of proteins with unknown function appears to be restricted to Bacillaceae.
Organ specific protein (Organ_specific_prot)
Type: Family

This eukaryotic family includes a number of plant organ-specific proteins. While their function is unknown, their predicted amino acid sequence suggests that these proteins could be exported and glycosylated .
Protein of unknown function DUF2759 (DUF2759)
Type: Family

This family of proteins with unknown function appear to be restricted to Bacillales.
Selenoprotein SelK/SelG (Se_SelK/SelG)
Type: Family

This entry represents an eukaryotic family of selenoproteins. It includes SelK, which seems to play an important role in protecting cells from endoplasmic reticulum stress-induced apoptosis . It is required for Ca2+ flux in immune cells and plays a role in T-cell proliferation and in T-cell and neutrophil migration . SelK is also required for palmitoylation of some proteins which regulates its stability and function . SelG, which may be involved in regulating the redox state of the cell .
Protein of unknown function DUF2764 (DUF2764)
Type: Family

This bacterial family of proteins has no known function.
Fumarase D (FumD)
Type: Family

Fumarase D (YdhZ) catalyzes in vitro the addition of water to fumarate, forming malate .
Protein of unknown function DUF2770 (DUF2770)
Type: Family

Members in this family of proteins from Enterobacteria are annotated as YceO; however, currently no function is known.
Protein of unknown function DUF2771 (DUF2771)
Type: Family

This bacterial family of proteins has no known function.
Spore germination protein GerPE (Spore_germ_GerPE)
Type: Family

GerPE is required for the formation of functionally normal spores. It could be involved in the establishment of a normal spore coat structure and/or permeability, which allows the access of germinants to their receptor .
Protein of unknown function DUF2773 (DUF2773)
Type: Family

This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Domain of unknown function DUF2786 (DUF2786)
Type: Domain

This domain is found in proteins that have no known function.
Mbeg1-like (Mbeg1-like)
Type: Family

This family includes a group of uncharacterised proteins from bacteria. Recently, a member from Gemella sanguinis M325, Mbeg1 (for "microbiome bacteria effector gene") has been identified as the first example of this protein family being associated with a potential effector function in the human microbiome .
Domain of unknown function DUF3074 (DUF3074)
Type: Domain

This domain defines a eukaryotic family of proteins that have no known function but appear to be part of the START superfamily.
Protein of unknown function DUF3141 (DUF3141)
Type: Family

This family of proteins appears to be predominantly expressed in Proteobacteria. Their function is unknown.
Protein of unknown function DUF3194 (DUF3194)
Type: Family

Proteins in this family contain a novel α+β fold, consisting of two α-helices (one N-terminal and one C-terminal) packed on the same side of a central β-hairpin . They share the structural similarity to Escherichia coli MinE, a protein which controls that division occurs at the midcell site . A hypothetical protein from Methanobacterium thermoautotrophicum (Mth), Mth677, is included in this entry.
Protein of unknown function DUF3196 (DUF3196)
Type: Family

The entry comprises bacterial proteins of unknown function. One of the proteins in this entry, MPN330, is thought to involved in a cellular function that has yet to be characterised. The protein has 11 helices and a novel fold. No function is currently known for this protein.
Uncharacterised membrane protein Ta0354, soluble domain (Unchr_Ta0354_soluble_domain)
Type: Domain

This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.
Protein of unknown function DUF3201 (DUF3201)
Type: Family

This archaeal family of proteins has no known function.
Protein of unknown function DUF3217 (DUF3217)
Type: Family

This family of proteins with unknown function appears to be restricted to Mycoplasma and Ruminococcus spp. The structure of Uncharacterized protein MG376 homologue from Mycoplasma pneumoniae shows an OB fold with six β-strands and three loops forming a β-barrel that is capped by one α-helix . Its specific function is still unknown.
AtzH-like (AtzH-like)
Type: Family

This entry represents a family of bacterial proteins previously known as DUF3225, including AtzH from Pseudomonas sp. (

). AtzH is thought to be an amidase responsible for converting 1,3-dicarboxyurea to allophanate. This protein, which adopts a dimeric assembly, shows a seven-stranded anti-parallel β-sheet and three helices .
Protein of unknown function DUF3226 (DUF3226)
Type: Family

This entry represents a family of functionally uncharacterised prokaryotic proteins.
Anti-lipopolysaccharide factor/Scygonadin (Anti-LPS_factor/Scygonadin)
Type: Family

Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria . This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus .
Protein of unknown function DUF2589 (DUF2589)
Type: Family

This family of proteins has no known function.
WD repeat-containing and planar cell polarity effector protein Fritz (Frtz)
Type: Family

Fritz is a probable effector of the planar cell polarity signaling pathway which regulates the septin cytoskeleton in both ciliogenesis and collective cell movements. In Drosophila melanogaster, fritz regulates both the location and the number of wing cell prehair initiation sites .
Small subunit of serine palmitoyltransferase-like (Ser_palmitoyltrfase_ssu-like)
Type: Family

Serine palmitoyltransferase (SPT) catalyzes the first committed step in sphingolipid biosynthesis. In mammals, two small subunits of serine palmitoyltransferase, ssSPTa and ssSPTb, substantially enhance the activity of SPT, conferring full enzyme activity upon it . The 2 ssSPT isoforms share a conserved hydrophobic central domain, which is predicted to reside in the membrane.

This entry represents the small subunits of serine palmitoyltransferase. It also includes a number of putative uncharacterised proteins from fungi and plants.
Protein of unknown function DUF3334 (DUF3334)
Type: Family

This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Domain of unknown function DUF3388 (DUF3388)
Type: Domain

This domain is found in a family of bacterial proteins that are functionally uncharacterised. Proteins in this family are typically between 261 to 275 amino acids in length and have a N-terminal ACT domain.
Protein of unknown function DUF3397 (DUF3397)
Type: Family

This family of bacterial proteins is currently functionally uncharacterised.
Mammalian cell entry, C-terminal (Mce_C)
Type: Domain

This entry represents a domain of unknown function found at the C terminus of many proteins in the mammalian cell entry family.
Glycogen phosphorylase, domain of unknown function DUF3417 (Glycogen_phosphorylase_DUF3417)
Type: Domain

This domain of unknown function is found at the N terminus of members of the glycogen phosphorylase family.
Inverse autotransporter, beta-domain (IAT_beta)
Type: Domain

This domain is found in a group of β-barrel porin-like outer membrane proteins from enteropathogenic Gram-negative bacteria. Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They carry C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal beta domains that are embedded in the outer membrane. This entry represents the β-barrel porin-like domain in the outer membrane that can be found in intimins, invasins and other inverse autotransporters .

Intimin is believed to mediate adherence and it is necessary for the production of attaching and effacing lesions on tissue culture cells . Invasin is a protein that allows enteric bacteria to penetrate cultured mammalian cells . The entry of invasin in the cell is mediated by binding several beta-1 chain integrins .
Protein of unknown function DUF3558 (DUF3558)
Type: Family

This family of bacterial proteins includes members annotated as putative lipoprotein lprB. However, their function is unknown.
Arsenosugar biosynthesis radical SAM protein ArsS-like, C-terminal domain (ArsS-like_C)
Type: Domain

This domain at the C-terminal end of Slr0304 protein from Synechocystis sp. PCC 6803 (

) and Slr3097 protein from Nostoc sp. PCC 7120 (

), which were named in 2019 as ArsS, a radical SAM enzyme involved in arsenosugar biosynthesis . This domain has several conserved Cys residues, one of which is replaced by selenocysteine in at least five bacterial reference genomes. It is found in association with an N-terminal radical_SAM domain (

). Members of this group are predominantly found in bacterial proteins.
Protein of unknown function DUF3789 (DUF3789)
Type: Family

This family of functionally uncharacterised bacterial proteins are approximately 40 amino acids in length. They contain two completely conserved residues (V and C) that may be functionally important.
Protein of unknown function DUF3793 (DUF3793)
Type: Family

This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Protein of unknown function DUF3800 (DUF3800)
Type: Family

This family of proteins is functionally uncharacterised. Some family members possess a DE motif at their N terminus and a QXXD motif at their C terminus that may be functionally important.
Protein of unknown function DUF3804 (DUF3804)
Type: Family

Structural alignments indicate that this family of functionally uncharacterised proteins carry an NTF2-fold with a hydrophobic cavity. Family members also contain two highly conserved tryptophan residues toward their C-terminal ends.
Protein of unknown function DUF3807 (DUF3807)
Type: Family

This is a family of conserved fungal proteins of unknown function.