SII-SWORD/CoKE huggingface dataset:
Collagen type XV/XVIII, trimerization domain (XV/XVIII_trimerization_dom)
Type: Domain

Collagens XV and XVIII are members of the multiplexin family and are homo-trimers comprising a single alpha-chain with a central highly interrupted collagenous domain flanked by N- and C-terminal non collagenous domains (NC). Type XVIII is a heparan sulfate proteoglycan that localizes in epidermal and vascular basement membrane, whereas type XV can carry chondroitin/dermatan sulfate alone or chondroitin/dermatan sulfate and heparan sulfate chains which localizes to areas peripheral to basement membranes and associates directly with collagen fibers/fibrils in a manner consistent with other chondroitin sulfate proteoglycans .

The highest level of sequence homology between these two types of collagens lies in their NC1 domain, organized into a trimerization domain, a hinge region and an endostatin domain. This entry represents the small trimerization domain from Collagens type XV and XVIII, which has high structural conservation, despite low sequence identity .
F-box protein Hrt3/FBXO9, C-terminal (Hrt3/FBXO9_C)
Type: Domain

This entry represents a domain in the C-terminal region of several F-box proteins in eukaryotes. These proteins are the substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Proteins containing this domain include the yeast Hrt3 protein and human F-box only 9 protein (FBXO9) .
Transcriptional regulator-like domain (Trans_reg_dom)
Type: Domain

This domain, previously known as DUF6499, is found in transcriptional regulators and similar proteins mainly found in proteobacteria . This domain is found in association with the DNA binding domain

in many proteins. It is predicted to adopt an all-α structure.
Protein of unknown function DUF6498 (DUF6498)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea.
Protein of unknown function DUF6497 (DUF6497)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6496 (DUF6496)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses.
Nis1-like (Nis1)
Type: Family

Necrosis-inducing secreted protein 1 (Nis1) is a fungal secreted effector that induces necrotic lesions in plants it infects . This protein interacts with the host receptor-like kinases and inhibits their kinase activity .
Protein of unknown function DUF6495 (DUF6495)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6494 (DUF6494)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. There is a conserved SQREIE sequence motif.
Domain of unknown function DUF6493 (DUF6493)
Type: Domain

This presumed domain is functionally uncharacterised. This domain can be found in proteins from bacteria.
Sphingomyelin phosphodiesterase, C-terminal domain (ASM_C)
Type: Domain

This entry represents the C-terminal domain found in acid sphingomyelin phosphodiesterases mostly from eukaryotes.

Human sphingomyelin phosphodiesterase converts sphingomyelin to ceramide and plays an important role in the export of cholesterol from the intraendolysosomal membranes . When secreted, modulates cell signaling and, upon infection, takes an important part in the host defense . Its three-dimensional structure has been resolved, and it has been linked to the Niemann-Pick disease .
GEVED domain (GEVED)
Type: Domain

This presumed domain is found in the CshA protein from Streptococcus gordonii. The domain is named after the sequence found in CshA in the conserved C-terminal region. The conserved negatively charged residues suggest that this domain may bind to calcium ions. This domain is part of the non-repetitive region NR3 .
Inactive STAND domain (iSTAND)
Type: Domain

This is the inactive P-loop NTPase domain of AAA+ NTPases that belong to the STAND subfamily known as inactive STAND (iSTAND). iSTAND is a component of the MoxR-vWA-iSTAND ternary systems of NTP-dependent conflict systems. The iSTAND component shows clear architectural parallels to the VMAP of the vWA-MoxR-VMAP systems .
JAB-N domain (FvmJAB_N)
Type: Domain

This domain is observed N-terminal to JAB deubiquitinase in the Ub system component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems .
FtsH ternary systems, vWA domain (ivWA)
Type: Domain

This entry represents the highly-divergent vWA domain lacking metal-chelating aspartates of typical vWA domains. It is the core component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems .
Exportin-5, C-terminal domain (Exportin-5_C)
Type: Domain

This entry represents the C-terminal domain found in eukaryotic proteins such as Exportin-5 from mammals, HASTY 1 from Arabidopsis and Msn5 from yeasts.

Exportin-5 mediates the nuclear export of proteins bearing a double-stranded RNA binding domain (dsRBD) and double-stranded RNAs (cargos). It also mediates the nuclear export of micro-RNA precursors, which form short hairpins and micro-RNA precursors, which form short hairpins and, in some circumstances, it can also mediate the nuclear export of deacylated and aminoacylated tRNAs. .
FtsH ternary system vWA domain, fused N-terminal helical region (ivWA-helical_N)
Type: Domain

This entry represents a functionally uncharacterised helical domain fused at the N terminus of the ivWA domain, a core component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems .
FtsH ternary system domain X1 (fvmX1)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems .
FtsH ternary system domain X3 (fvmX3)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems .
FtsH ternary system domain X2 (fvmX2)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems .
FtsH ternary system domain X3-analog (fvmX3-analog)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. This domain is positionally-equivalent and mutually-exclusive to the fvmX3 domain in gene neighbourhoods .
FtsH ternary system domain X5 (fvmX5)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems .
FtsH ternary system domain X6 (fvmX6)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems .
FtsH ternary system domain X7 (fvmX7)
Type: Domain

This is an uncharacterised domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems .
YukD-like, N-terminal domain (fvmYukD-like_N)
Type: Domain

This is an uncharacterised domain found N-terminal to the YukD-like ubiquitin domain in FtsH ternary systems, a class of NTP-dependent biological conflict systems .
FtsH ternary system-associated peptide (fvmRadSAM-pep)
Type: Family

This entry represents a predicted peptide-effector encoded as standalone domain in some FtsH ternary system neighborhoods. It is likely modified by the Radical SAM domain also found in these neighbourhoods. The FtsH ternary systems are a class of NTP-dependent biological conflict systems .
Domain of unknown function DUF6429 (DUF6429)
Type: Domain

This domain of unknown function is found in uncharacterised bacterial proteins. This domain is about 50 amino acids in length and contains the conserved WK, RS and TxxG sequence motifs.
Protein of unknown function DUF6432 (DUF6432)
Type: Family

This family of proteins found in archaea is functionally uncharacterised. Members of this entry are thought to be transcriptional regulators.
Protein of unknown function DUF6433 (DUF6433)
Type: Family

This family of proteins is functionally uncharacterised, mainly found in phages. They contain the conserved NFD and LEGL motifs.
Domain of unknown function DUF6434 (DUF6434)
Type: Domain

This domain of unknown function is found in uncharacterised proteins from bacteria. There are three conserved motifs: TxI/V, RxFF and FxF, and a conserved W/Y residue at the C-terminal.
Protein of unknown function DUF6435 (DUF6435)
Type: Family

This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are approximately 60 amino acids in length and are predicted to have a coiled-coil structure. There are two conserved motifs: KxLxxxY and EA.
Domain of unknown function DUF6436 (DUF6436)
Type: Domain

This domain of unknown function is found in uncharacterised bacterial proteins. This domain is about 60 amino acids in length and contains the conserved motifs GPY, GxxC and GCxC. These conserved cysteine residues and the fact that this domain has overlaps with families in Pfam clan CL0172 suggest that proteins containing this domain are related to thioredoxins and are likely to be thiol-disulfide isomerases.
PI4-kinase, N-terminal (PI4K_N)
Type: Domain

This entry represents a non-catalytic region in eukaryotic phosphatidylinositol 4-kinase alpha (PI4K) proteins. These proteins play a role in the production of the second messenger inositol-1,4,5-trisphosphate . In human PI4K alpha, this domain consists of a long sequence found in the N-terminal region of the protein. This region forms a large alpha solenoid structure .
Domain of unknown function DUF64370 (DUF6437)
Type: Domain

This domain is functionally uncharacterised. It is found in alphaproteobacteria.
Domain of unknown function DUF6438 (DUF6438)
Type: Domain

This domain of unknown function is found in uncharacterised proteins from bacteria and archaea. This domain is about 75 amino acids in length and it contains the conserved motif CxxxGxCP. Towards the C terminus there are two conserved residues, a glycine and an aspartate. Some proteins containing this domain also have an ankyrin repeat-containing region.
HflX, C-terminal domain (HflX_C)
Type: Domain

This entry represents the C-terminal domain of GTPase HflX from Escherichia coli .

HflX is a GTPase that associates with the 50S ribosomal subunit. Its C-terminal domain (CTD) predominantly interacts with the N-terminal domain of uL11 at the bL12 stalk base. Truncation of the CTD rendered HflX inactive in 70S splitting . HflX may play a role in the rescuing of heat-damaged ribosomes and in the improvement of cell survival .
Protein of unknown function DUF6492 (DUF6492)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes.
Protein of unknown function DUF6491 (DUF6491)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6490 (DUF6490)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in plants.
Protein of unknown function DUF6489 (DUF6489)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6488 (DUF6488)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Domain of unknown function DUF6487 (DUF6487)
Type: Domain

This is an uncharacterised domain found in bacterial proteins. This domain is likely to be a zinc-binding domain.
Protein of unknown function DUF6486 (DUF6486)
Type: Family

This entry represents a group of uncharacterised bacterial proteins. There is a conserved IAVASA sequence motif.
Domain of unknown function DUF6484 (DUF6484)
Type: Domain

This domain of unknown function is found in uncharacterised proteins mostly from Proteobacteria. Many proteins containing this domain are related to the Type VI secretion system and to Phage-related baseplate proteins.
Protein of unknown function DUF6483 (DUF6483)
Type: Family

This is a family of bacterial proteins, functionally uncharacterised.
Protein of unknown function DUF6482 (DUF6482)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
HD-associated domain (HD_assoc_2)
Type: Domain

This entry represents a domain that is found C-terminal to the HD domain found in the EF1143 protein (

) and O67745_AQUAE (

) . According to the Aravind-Koonin classification of HD-domain proteins, proteins containing this domain belong to cluster 1 .
Protein of unknown function DUF6481 (DUF6481)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6439 (DUF6439)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria.
Protein of unknown function DUF6480 (DUF6480)
Type: Family

This is a family of bacterial proteins, functionally uncharacterised.
Protein of unknown function DUF6479 (DUF6479)
Type: Family

This family of proteins found in bacteria is functionally uncharacterised.
Protein of unknown function DUF6478 (DUF6478)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Domain of unknown function DUF6440 (DUF6440)
Type: Domain

This domain is functionally uncharacterised, mainly found in proteins from Firmicutes but also from viruses. It contains three conserved motifs: RF, TGxxY and TPLLD.
Protein of unknown function DUF6477 (DUF6477)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Glyoxalase-related protein (Glyoxalase_8)
Type: Domain

This presumed domain is functionally uncharacterised. This domain is part of the Glyoxalase superfamily.
2EXR domain (2EXR)
Type: Domain

This entry represents a domain containing two conserved ExR motifs that may be functionally important. Protein containing this domain are mostly from fungi.
Protein of unknown function DUF6476 (DUF6476)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
GPAT/DHAPAT, C-terminal domain (GPAT/DHAPAT_C)
Type: Domain

This entry represents the C-terminal domain of glycerol-3-phosphate acyltransferases (GPATs) and dihydroxyacetone phosphate acyltransferases.

Dihydroxyacetonephosphate acyltransferase (DHAPAT) catalyses the first step in the biosynthesis of ether phospholipid plasmalogen, and may play also a significant role in nonether glycerolipid biosynthesis . In humans, mutations in DHAPAT results in the genetic disorder rhizomelic chondrodysplasia punctata type 2, characterised by rhizomelic shortening of femur and humerus, cataract,and severe mental retardation .

This entry includes PlsB, a GPAT from E. coli in which membrane synthesis depends on allosteric control of this enzyme. PlsB regulation plays an important role in the phospholipid synthesis pathway and is part of the response to certain stress signals . In many other bacteria, PlsB is not found, and appears to be replaced by a two enzyme system for 1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y system

.

GPATs are classified into four isoforms in mammals; GPAT1 and GPAT2 are localized in the mitochondrial outer membrane, whereas GPAT3 and GPAT4 are localized in the endoplasmic reticulum membrane . This entry includes the mitochondrial isoform GPAT.
Domain of unknown function DUF6475 (DUF6475)
Type: Domain

This presumed domain is functionally uncharacterised. Proteins containing this domain are found mainly in Proteobacteria and viruses. It contains the conserved motifs FDD and MGGW.
Protein of unknown function DUF6474 (DUF6474)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
GTPase-associated system helical domain (GASH)
Type: Domain

This entry represents a helical domain observed in the GAP1-N1 type of GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. GASH is one component of the GTPase-activated complex in these systems, potentially involved in the sensing of invasive elements .
Domain of unknown function DUF6473 (DUF6473)
Type: Domain

This presumed domain is functionally uncharacterised.
Domain of unknown function DUF6472 (DUF6472)
Type: Domain

This domain found is functionally uncharacterised. It contains 4 conserved cysteines.
Domain of unknown function DUF6471 (DUF6471)
Type: Domain

This domain of unknown function is found in uncharacterised proteins mostly from bacteria (predominantly Proteobacteria). There is a conserved motif KxxRG and a highly conserved L residue. It may be a DNA-binding domain.
Protein of unknown function DUF6470 (DUF6470)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, predominantly in Firmicutes. There is a conserved ID motif.
Double-GTPase 2 (DO-GTPase2)
Type: Domain

This domain is known as DO-GTPase2. The majority of DO-GTPases 2 have 1-2 N-terminal zinc ribbons (ZnR), while a reduced proportion have N-terminal TM segments .

Protein containing this domain are GTPases of a GTPase-centric, NTP-dependent ternary systems. This domain belongs to a previously unrecognised TRAFAC clade with a conserved glutamate in its Walker B motif. In 38% of these systems they occur as two paralogous copies suggesting that they function as dimers, and accordingly, they were named as double-GTPases (DO-GTPases) .
Domain of unknown function DUF6469 (DUF6469)
Type: Domain

This presumed domain can be found in plant proteins. It is found in hypothetical UvrD-like helicases and related sequences, all containing a P-loop motif that is characteristic of the AAA superfamily. This domain is located towards to the N terminus, adjacent to the AAA domain. There are two conserved motifs, GD and RIW. There is also a highly conserved D residue.
Double-GTPase 1 (DO-GTPase1)
Type: Domain

This domain is known as DO-GTPase1.

Protein containing this domain are GTPases of a GTPase-centric, NTP-dependent ternary systems. This domain belongs to a previously unrecognised TRAFAC clade with a conserved glutamate in its Walker B motif. In 38% of these systems they occur as two paralogous copies suggesting that they function as dimers, and accordingly, they were named as double-GTPases (DO-GTPases) .
Domain of unknown function DUF6468 (DUF6468)
Type: Domain

This domain of unknown function is found in uncharacterised proteins predominantly from Alphaproteobacteria.
GTPase-associated adaptor domain (GAAD)
Type: Domain

This entry represents an adaptor domain in the GTPase-centric systems of NTP-dependent conflict systems that directly couples the effector to the GAP1 component . It is predicted to adopt an α-helical fold.
Protein of unknown function DUF6428 (DUF6428)
Type: Family

This family of proteins found in bacteria is functionally uncharacterised. There are two conserved sequence motifs, DCGG and QLW, and conserved cysteine residues at the C terminus.
Thoeris protein ThsA, Macro domain (ThsA_Macro)
Type: Domain

Thoeris is a bacterial antiphage defense system, which consists of two genes, thsA and thsB, via NAD+ degradation . ThsA has robust NAD+ cleavage activity and a two-domain architecture containing an N-terminal NAD-binding domain (denoted as sirtuin-like or Macro) and C-terminal SLOG-like domain. In some instances, such as in B. amyloliquefaciens, ThsA has an N-terminal transmembrane domain . ThsB (also referred to as TIR1 and TIR2) is structurally similar to TIR domain proteins but without enzymatic activity.

This entry represents the C-terminal Macro domain of ThsA from B. amyloliquefaciens, which adopts a Rossmann-like fold and binds NAD+ .
Domain of unknown function DUF6431 (DUF6431)
Type: Domain

This domain of unknown function is found in uncharacterised protein mostly from bacteria. This domain is about 90 amino acids in length. It contains the conserved sequences CxxC, RxxCxxxxC and a conserved LP motif.
La-related protein 7 homolog, xRRM domain (Lar7_xRRM)
Type: Domain

This is the atypical RRM (xRRM) domain found in a group of fungal proteins, including La-related protein 7 homolog (Lar7, also known as Pof8) from Schizosaccharomyces pombe, a member of the ancient superfamily of La and La-related proteins (LaRPs) . Lar7 is a RNA-binding protein required for assembly of the holoenzyme telomerase ribonucleoprotein (RNP) complex. It binds telomerase RNA (TER1) and promotes assembly of TER1 with catalytic subunit of telomerase reverse transcriptase (Trt1) .
Contractile injection system tape measure protein (CIS_TMP)
Type: Family

Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. This entry represents a group of proteins found mostly in bacteria as part of the Photorhabdus virulence cassette (PVC), one group of extracellular CISs .

This protein is the tape measure which dictates the length of the syringe tail. It is found in low copy number and is most likely not present in the mature syringes. Deletion of the tape measure protein Pvc14 from P. asymbiotica resulted in large variations in the length of the syringes . The N and C-terminal domains of these proteins are well conserved, but they have a wide length variation in the central region.
Tail virion protein G7P (Inovirus_G7P_2)
Type: Family

Tail virion protein 7P (G7P) is a viral transmembrane protein that interacts with the packaging signal of the viral genome leading to the initiation the virion concomitant assembly-budding process in the host inner membrane . The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
YegS/DAGK, C-terminal domain (YegS/DAGK_C)
Type: Domain

This entry represents the C-terminal domain of putative lipid kinase YegS and diacylglycerol kinase DAGK from bacteria . This domain can also be found in eukaryotic sphingosine kinases, such as sphingosine kinase 2 from animals and plants .

This domain is related to the β sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site cleft found between the two domains. The C-terminal domain contains 13 β-strands and two α-helices. The likely substrate for YegS is phosphatidylglycerol .
Ternary complex associated domain 2 (TCAD2)
Type: Domain

This entry represents a novel uncharacterised domain found associated with the vWA-MoxR-VMAP ternary systems .
Ternary complex associated domain 3 (TCAD3)
Type: Domain

This entry represents a novel uncharacterised domain found associated with the vWA-MoxR-VMAP ternary systems . This domain is found in cyanobacteria.
Ternary complex associated domain 7 (TCAD7)
Type: Domain

This entry represents a novel uncharacterised domain found associated with the vWA-MoxR-VMAP ternary systems .
Ternary complex associated domain 9 (TCAD9)
Type: Domain

This entry represents a novel uncharacterised domain found associated with the vWA-MoxR-VMAP ternary systems . This domain is likely a phosphotransferase enzyme.
Phytanoyl-CoA hydroxylase-interacting protein-like, C-terminal (PHYIP/PHIPL_C)
Type: Domain

This entry represents the C-terminal domain found in Phytanoyl-CoA hydroxylase-interacting protein (PHYIP/PAHX-AP1) and Phytanoyl-CoA hydroxylase-interacting protein-like (PHIPL) from animals. PHYIP interacts with the C-terminal domain of dual-specificity tyrosine-phosphorylated and regulated kinase 1A (DYRK1A) and may contribute to new cellular functions of DYRK1A, playing a role in the development of the central system .