SII-SWORD/CoKE huggingface dataset:
Ancillary SecYEG translocon subunit/Cell division coordinator CpoB, TPR domain (SecYEG/CpoB_TPR)
Type: Domain

This is the TPR domain found in ancillary SecYEG translocon subunit and cell division coordinator CpoB.

CpoB coordinates the complexes involved in septal peptidoglycan synthesis (PBP1B-LpoB complex) and outer membrane constriction (Tol system), which contributes to maintain the integrity of the cell envelope during division .

YfgM is a subunit of the ancillary SecYEG translocon that may mediate protein transfer from the SecYEG translocon to the periplasmic chaperone network via its periplasmic C-terminal region .
Domain of unknown function DUF2134, membrane (DUF2134_membrane)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins, is likely to be involved in Flp pilus biogenesis.
Protein of unknown function DUF2214, membrane (DUF2214_membrane)
Type: Family

This family has no known function.
Lipid A deacylase LpxR (LpxR)
Type: Family

This entry represents a group of bacterial proteins that include the lipid A deacylase LpxR from Salmonella typhimurium. LpxR is an outer membrane protein that catalyses the removal of the the 3'-acyloxyacyl moiety from lipid A. It requires Ca2+ for its activity. This enzyme folds into a 12-stranded antiparallel β-barrel with the N- and C- terminal ends pointing towards the periplasm and three extracellular loops consisting of α-helical regions at the opposite side of the β-barrel .
Protein of unknown function DUF2225 (DUF2225)
Type: Family

This conserved bacterial family has no known function.
CoA enzyme activase, domain of unknown function DUF2229 (CoA_activase_DUF2229)
Type: Domain

Proteins containing this domain include various bacterial hypothetical proteins, as well as CoA enzyme activases. The exact function of this domain has not, as yet, been defined.
Protein of unknown function DUF2232 (DUF2232)
Type: Family

This family of bacterial and eukaryotic proteins has no known fucntion.
Phosphodiester glycosidase (NAGPA)
Type: Domain

This domain can be found in many bacterial and several viral proteins and can be identified in the mammalian transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA). Some proteins containing this domain may function as phosphodiester glycosidases .
T6SS, Phospholipase effector Tle1-like, catalytic domain (Tle1-like_cat)
Type: Domain

This entry represents a domain found in the type VI secretion system (T6SS) Phospholipase effector Tle1 from Pseudomonas aeruginosa (

) and similar bacterial and fungal sequences. Tle1, which hydrolyse membrane phospholipids, is organised into two distinct parts, the phospholipase catalytic module (this entry) and the putative membrane-anchoring module (

). This domain adopts a compact conformation with a classical mixed α/β-hydrolase fold that shows of seven central parallel β-sheets and 13 α-helices .
ER-bound oxygenase mpaB/mpaB'/Rubber oxygenase, catalytic domain (MPAB/Lcp_cat_dom)
Type: Domain

This entry represents the catalytic domain found in the endoplasmic reticulum (ER)-bound oxygenases mpaB' (MPAB2) and mpaB (MPAB) from Penicillium brevicompactum and Penicillium roqueforti and in the rubber oxygenase (Lcp) from Streptomyces sp., which contains highly conserved arginine and histidine residues. Structural analysis from Lcp revealed that Arg164, Thr168 and His198 are crucial active site residues . The ER-bound oxygenases mpaB and mpaB' are part of the gene cluster that mediates the biosynthesis of mycophenolic acid (MPA) and mediates the oxidative cleavage the C19-C20 double bond in farnesyl-DHMP (FDHMP) to yield FDHMP-3C via a mycophenolic aldehyde intermediate . Rubber oxygenase Lcp (Latex clearing proteins) is a rubber oxygenase that catalyses the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria such as Streptomyces sp. K30 . This domain is also present in uncharacterised proteins from Mycobacterium sp. and hypothetical proteins, mainly from bacteria and fungi.
Protein of unknown function DUF2237 (DUF2237)
Type: Family

This family of hypothetical proteins has no known function.
Protein of unknown function DUF2239 (DUF2239)
Type: Family

This family of uncharacterised bacterial proteins has no known function.
Protein of unknown function DUF2240 (DUF2240)
Type: Family

This family of various hypothetical archaeal proteins with no known function.
Domain of unknown function DUF2241 (DUF2241)
Type: Domain

This entry represents a domain of unknown function frequently found at the N-terminal end of a group of proteins mainly from bacteria and fungi. Its structure is similar to the ACT domain which suggests that it might bind to amino acids and regulate other protein activity.
Protein of unknown function DUF2242 (DUF2242)
Type: Family

This family includes putative lipoproteins and uncharacterised proteins.
Protein of unknown function DUF2243, membrane (DUF2243_membrane)
Type: Family

This entry includes membrane proteins of unknown function.
Domain of unknown function DUF2249 (DUF2249)
Type: Domain

This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see

).
Protein of unknown function DUF2252 (DUF2252)
Type: Family

DUF2252 has no known function.
Protein of unknown function DUF2254, membrane (DUF2254_membrane)
Type: Family

Members of this family of proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined.
2OG-Fe dioxygenase (2OG-Fe_dioxygenase)
Type: Family

This family contains Fe-dependent dioxygenases, including L-isoleucine dioxygenase (IDO) , 3(1)-hydroxy-L-isoleucine 4-dioxygenase (HilB) and Bifunctional enzyme flvA .
Protein of unknown function DUF2259, secreted (DUF2259_secreted)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Protein of unknown function DUF2267 (DUF2267)
Type: Family

This entry contains proteins that have no known function.
Domain of unknown function DUF2268 (DUF2268)
Type: Domain

This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Protein of unknown function DUF2269, transmembrane (DUF2269_transmembrane)
Type: Family

Members of this family of bacterial hypothetical integral membrane proteins have no known function.
Protein of unknown function DUF2273 (DUF2273)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Autophagy-related protein 13, N-terminal (Atg13_N)
Type: Domain

This entry represents the N-terminal domain of autophagy-related protein 13 (Atg13) from yeasts, animals and plants. They function in autophagy.

Fission yeast autophagy initiation is controlled by the Atg1 kinase complex, which is composed of the Ser/Thr kinase Atg1, the adaptor protein Atg13, and the ternary complex of Atg17-Atg31-Atg29. Atg13 recruits Atg1 to the site of autophagosome formation and enhancing Atg1 kinase activity. Atg13 may have additional functions that are independent of a direct interaction or permanent colocalization with Atg1 .
Dpy-19/Dpy-19-like (Dpy-19/Dpy-19-like)
Type: Family

This entry represents the Dpy-19 protein from Caenorhabditis elegans and its homologues in other Metazoa, including mammals. In C. elegans, Dpy-19 is required to orient neuroblasts QL and QR correctly on the anterior/posterior (A/P) axis. These neuroblasts are born in the same A/P position, but polarise and migrate left/right asymmetrically, where QL migrates toward the posterior and QR migrates toward the anterior. After their migrations, QL (but not QR) switches on the Hox gene mab-5. Dpy-19 is required along with Unc-40 to express Mab-5 correctly in the Q cell descendants .
Protein of unknown function DUF2274 (DUF2274)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Domain of unknown function DUF2275 (DUF2275)
Type: Domain

This domain, found in various hypothetical bacterial proteins and in the RNA polymerase sigma factor, has no known function.
Protein of unknown function DUF2277 (DUF2277)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Protein of unknown function DUF2279, periplasmic lipoprotein (DUF2279_periplasmic_lipo)
Type: Family

This domain has no known function.
Protein LIN52 (DREAM_LIN52)
Type: Family

LIN52 is a component of the DREAM (MuvB/DRM) complex which represses cell cycle-dependent genes in quiescent cells and plays a role in the cell cycle-dependent activation of G2/M genes .
Protein of unknown function DUF2280 (DUF2280)
Type: Family

This entry includes Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Domain of unknown function DUF2281 (DUF2281)
Type: Domain

This domain is found in putative uncharacterised proteins, though some proteins contaning this domain are described as a transcritional regulator of the Xre family.
Protein of unknown function DUF2282, integral membrane (DUF2282_membr)
Type: Family

Members of this family of hypothetical bacterial proteins and putative signal peptide proteins have no known function.
Protein of unknown function DUF2288 (DUF2288)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Protein of unknown function DUF2290 (DUF2290)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Protein of unknown function DUF2292 (DUF2292)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Domain of unknown function DUF2293 (DUF2293)
Type: Domain

Proteins in this entry are found the bacteria and fungi, they have no known function.
Na+-translocating membrane potential-generating system MpsC (MpsC)
Type: Domain

This entry corresponds to the Na+-translocating membrane potential-generating system subunit MpsC .
Protein of unknown function DUF2298 (DUF2298)
Type: Family

Members of this highly hydrophobic probable integral membrane family belong to two classes. In one, a single copy of the region modelled by the signatures in this entry represents essentially the full length of a strongly hydrophobic protein of about 700 to 900 residues (variable because of long inserts in some). The domain architecture of the other class consists of an additional N-terminal region, two copies of the region represented by this model, and three to four repeats of TPR, or tetratricopeptide repeat. The unusual species range includes several Archaea, several Chloroflexi, and Clostridium phytofermentans. An unusual motif YYYxG is present. The function is unknown.
Protein of unknown function DUF2299 (DUF2299)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Domain of unknown function DUF2300, secreted (DUF2300_secreted)
Type: Domain

This domain, found in various bacterial hypothetical and putative signal peptide proteins, has no known function.
Protein of unknown function DUF2306, membrane (DUF2306_membrane)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Probable inorganic carbon transporter subunit DabA (DabA)
Type: Family

This entry represents the probable inorganic carbon transporter subunit DabA, which is part of an energy-coupled inorganic carbon pump together with DabB subunit in DAB operons (DAB1 and DAB2), found in a wide range of bacteria and archaea. DAB operon is required for CO2 concentrating mechanisms . The substrate of this subunit may be CO2 rather than carbonate ions based on kinetic calculations and in experimental assays in which E.coli was deleted of its carbonic anhydrase genes and expression of DAB2 operon restores its growth. Structural homology modelling suggests that DabA contains a domain that is distantly homologous to a type II beta-carbonic anhydrase (CA).
GapR-like (GapR-like)
Type: Family

GapR is a nucleoid-associated protein (NAP) critical for cellular function in Caulobacter crescentus (also known as Caulobacter vibrioides). Loss of GapR causes severe defects in growth, cell division, DNA replication, and chromosome segregation . This is a DNA-binding protein which has mainly an α-helical secondary structure. In the absence of DNA, GapR is a dimer, with each monomer folded into two extended α-helices, while in the presence of DNA, GapR forms a tetramer, with the C-terminal α-helix of each monomer reorganised into two shorter helices, which allows GapR to encircle the DNA .

This entry represents GapR-like from Caulobacter and similar proteins predominantly found in Alphaproteobacteria.
T6SS, Transcription factor RovC-like, DNA binding domain (RovC-like_DNA-bd)
Type: Domain

This domain is found in a group of proteins from proteobacteria, including the hexameric transcription factor from Yersinia pseudotuberculosis RovC, which is essential for the activation of one of the Type VI secretion systems of this organism (T6SS4). This domain folds into a distinct variant of the helix-turn-helix domain that shows an 'extended-turn' motif. It is responsible for DNA binding, participating in transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer .
Bacteriophage Mu-like, Gp48 (Phage_Mu_Gp48)
Type: Family

Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins, including Gp48 from Bacteriophage Mu and other Mu-like prophages such as FluMu .
Domain of unknown function DUF2314 (DUF2314)
Type: Domain

This domain of unkown function is found in various bacterial hypothetical proteins, as well as putative ankyrin repeat proteins.
Protein of unknown function DUF2316 (DUF2316)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Membrane iron-sulfur containing protein FtrD-like (FtrD-like)
Type: Domain

Proteins containing this domain are bacterial membrane proteins associated with the FTR1 protein, an homologous to FtrC in the FtrABCD complex. This complex is a ferric iron transporter in which the ferric iron is generated by ferrous oxidation that requires the electron transfer by iron-sulfur cluster-containing FrtD. Proteins containing this domain are part of the iron-sulfur-containing Rieske superfamily and are likely to have an analogous function to FtrD in iron transport .
Putative beta-barrel porin 2 (BBP2_2)
Type: Family

This entry represents a putative β-barrel porin type 2.
Domain of unknown function DUF2326 (DUF2326)
Type: Domain

This domain, found in bacterial proteins, has no known function.
Histidine phosphotransferase ChpT, C-terminal (ChpT_C)
Type: Domain

This entry represents the C-terminal domain of ChpT.
Protein of unknown function DUF2334 (DUF2334)
Type: Family

This entry represents Uncharacterized protein YdaL from Bacillus subtilis (strain 168) and similar proteins from bacteria and archaea. YdaL has been related to polysaccharide production .
Anti-sigma K factor RskA, C-terminal (RskA_C)
Type: Domain

This domain, formerly known as DUF2337, is found at the C-terminal end of the anti-sigma-K factor from Mycobacterium tuberculosis (RskA) and similar bacterial sequences.

RskA (regulator of sigma K) represses the extra-cytoplasmic function (ECF) sigma factor K (sigK) by binding to it and inhibiting its activity . This leads to a decreased expression of SigK-regulated genes, such as MPB70 and MPT83. RskA from Mycobacterium bovis is however probably dysfunctional, due to at least one of the two natural occurring polymorphisms in its encoding gene, when compared to M. tuberculosis . This leads to an increased expression of SigK-regulated genes.
Domain of unknown function DUF2341 (DUF2341)
Type: Domain

This domain of unknown function is found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins.
Zinicin-like metallopeptidase type 2 (Zinicin_2)
Type: Family

This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold . The structure of this family has similarity to Peptidase_M1 (

).
Brl1/Brr6 domain (Brl1/Brr6_dom)
Type: Domain

In Saccharomyces cerevisiae, Brr6 and Brl1 are interacting proteins that localise to the nuclear envelope and regulate lipid homeostasis . Mutation studies have implicated the proteins in nuclear pore complex biogenesis and mRNA nuclear export , although it may be that these observed effects are due to defects in maintaining the biophysical properties of the nuclear envelope .
Domain of unknown function DUF2344 (DUF2344)
Type: Domain

This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Type VI secretion system spike protein VgrG2, domain of unknown function DUF2345 (VgrG2_DUF2345)
Type: Domain

Type VI secretion system (T6SS) appears to be confined to Proteobacteria. It is important for bacterial pathogenesis, but it is also found in non-pathogenic bacteria, suggesting that T6SS involvement is not limited to virulence . T6SS was identified in Vibrio cholerae and Pseudomonas aeruginosa , and exports Hcp (Haemolysin-Coregulated Protein) and a class of proteins named Vgr (Val-Gly Repeats). In addition to Vgr and Hcp proteins, T6SS is characterised by the presence of an AAA+ Clp-like ATPase and of two additional genes icmF and dotU, encoding homologues of T4SS stabilising proteins .

Type VI secretion system spike protein VgrG2a and VgrG2b are homologous to (gp27)3-(gp5)3 phage-tail proteins, which is followed by a domain of unknown function (DUF2345). Unlike VgrG2a, VgrG2b belongs to a subclass of VgrG proteins, called evolved VgrGs that have an additional C-terminal extension with a putative zinc-dependent metallopeptidase domain. VrgG2b acts directly as an effector and promotes internalization by interacting with the host gamma-tubulin ring complex . It also elicits toxicity also in the bacterial periplasm and disrupts bacterial cell morphology. This toxicity is counteracted by a cognate immunity protein . In addition, it allows the delivery of the Tle3 antibacterial toxin to target cells where it exerts its toxicity .

This entry represents DUF2345, which is found in VgrG2a/b from Pseudomonas aeruginosa. This domain, present in both proteins, folds as a β-prism .
5-bromo-4-chloroindolyl phosphate hydrolysis protein (ChloroindolylP_hydrolase)
Type: Family

This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
PocR domain (PocR_dom)
Type: Domain

PocR, a ligand binding domain, has a novel variant of the PAS-like fold . Evidence suggests that it binds small hydrocarbon derivatives such as 1,3-propanediol .
Transcription activator HlyU (Transcription_activator_HlyU)
Type: Family

This is a family of hypothetical prokaryotic proteins, with no known function. One of the proteins in this entry corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members.
Methyltransferase regulatory domain, predicted (MeTrfase_reg_dom_prd)
Type: Domain

This entry represents a sequence region found in various prokaryotic methyltransferases that regulates the activity of the methyltransferase domain.
Bacteriophage Mu, GpT (Phage_Mu_GpT)
Type: Domain

This entry represents a conserved domain found in various caudoviral prophage proteins, including the bacteriophage Mu major head subunit GpT and related prophage.
RNA repair pathway DNA polymerase beta (RlaP)
Type: Family

This entry represents a group of proteins that belong to the DNA polymerase beta superfamily, with closest affinities to the Minimal Nucleotide Transferase clade (MNT). They are found in diverse RNA repair genome contexts centred on both RtcB and Rnl-type (ATP-grasp fold) repair ligases . Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Membrane protein, 6-pyruvoyl-tetrahydropterin synthase-related domain (Membrane_prot_PTPS-rel_domain)
Type: Domain

This entry is found in various bacterial and archaeal hypothetical membrane proteins, as well as in tetratricopeptide TPR_2 repeat protein. Its function has not yet been established, though it shows similarity to 6-pyruvoyl-tetrahydropterin synthase.
Replication initiator protein A (Replication_initiator_prot_A)
Type: Family

Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.
Type VII secretion system EssB (T7SS_EssB)
Type: Family

Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This protein is designated YukC in Bacillus subtilis and EssB is Staphylococcus aureus.
Single-stranded-DNA-specific exonuclease RecJ, C-terminal (RecJ_C)
Type: Domain

This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
BLOC-1-related complex subunit 5 (TBORCS5)
Type: Family

This entry includes the subunit 5 of the BLOC-1-related complex, which is also found in the BORC complex. BLOC-1 is important for the biogenesis of lysosome-related organelles, and BORC is important for the positioning of the lysosome in the cytoplasm. The BORC complex associates with the lysosomal membrane where it recruits the small GTPase Arl8, which leads in turn to the kinesin-dependent movement of lysosomes toward the plus ends of microtubules in the peripheral cytoplasm .
Transmembrane protein TPRA1/CAND2/CAND8 (TPRA1/CAND2/CAND8)
Type: Family

This family of membrane proteins are conserved from plants to humans, including CAND2 and CAND8 from Arabidopsis. CAND2 and CAND8 are predicted G-protein coupled receptors . CAND2 plays a role in plants and microbes interactions and acts as a phytomelatonin receptor that regulates stomatal closure through the Galpha subunit-mediated H2O2 production and Ca2 flux dynamics .
Essential MCU regulator, mitochondrial (MCU_reg)
Type: Family

Essential MCU regulator (EMRE) is a component of the mitochondrial calcium uniporter complex in metazoa, a complex that mediates calcium uptake into mitochondria. It bridges the calcium-sensing components of the complex, MICU1 and MICU2, and the pore-forming subunit MCU, and it is essential for the complex uniporter activity .
Transcription factor, enhancer of yellow 2 (TF_ENY2)
Type: Family

Enhancer of yellow 2 (EnY2) is a small transcription factor which is conserved from protozoa to humans . In insects it is known as enhancer of yellow 2 transcription factor, but in other organisms is known as transcription and mRNA export factor SUS1 or ENY2. It is involved in mRNA export coupled transcription activation by association with both the TREX-2 complex and the transcription regulatory histone acetylation complex SAGA . Within the SAGA complex, participates in a subcomplex that specifically deubiquitinates histone H2B . The TREX-2 complex participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery .
LLP homolog-like (LLPH-like)
Type: Family

This entry represents a family of LLP homolog (LLPH) animal proteins, including 18 kDa learning-associated protein of slug from Lehmannia marginata (LAPS18), which functions in the regulation of neuronal cell adhesion and/or movement and synapse attachment . It has been shown to bind to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activate the transcription of ApC/EBP mRNA . In mice hippocampal neurons, regulates dendritic and spine growth and synaptic transmission . In humans, LLPH plays a role in the ribosome biogenesis as one of the pre-60S assembly factors .