SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF5578 (DUF5578)
Type: Family

This is a family of unknown function found in Eukaryotes.
RPGRIP1, C-terminal (RPGRIP1_C)
Type: Domain

This is the C-terminal domain of retinitis pigmentosa G-protein regulator (RPGR) interacting protein-1 (RPGRIP1) present in Homo sapiens. A mutation in RPGRIP1 can be observed in the eye disease Leber congenital amaurosis. The domain is commonly known as the RPGR-interacting domain (RID) and is thought to have a C2-like fold .
Phage-Barnase-EndoU-ColicinE5/D-RelE-like nuclease (PBECR1)
Type: Domain

Polyvalent proteins are predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities .

This is a predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues .
DIS3-like exonuclease 2-like, C-terminal (Dis3l2-like_C)
Type: Domain

This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans .
Brr2, N-terminal helicase PWI domain (Brr2_helicase_PWI)
Type: Domain

This domain is found in spliceosomal RNA helicase Brr2 and its homologues. Brr2 is required for the assembly of a catalytically active spliceosome on a messenger RNA precursor. It plays an essential role in pre-mRNA splicing as a core component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes . Brr2 catalyses the ATP-dependent unwinding of U4/U6 RNA duplexes, an essential step in the assembly of a catalytically active spliceosome . The domain is found in the N-terminal region and is non-canonically PWI-like. The PWI-like domain is thought to be involved in protein-protein interactions .
Elongation Factor G, domain II (EFG_II)
Type: Domain

This entry represents domain II of elongation factor G (EFG). It shares a similar structure with domain V.

EF2 (or EFG) participates in the elongation phase of protein synthesis by promoting the GTP-dependent translocation of the peptidyl tRNA of the nascent protein chain from the A-site (acceptor site) to the P-site (peptidyl tRNA site) of the ribosome. EF2 also has a role after the termination phase of translation, where, together with the ribosomal recycling factor, it facilitates the release of tRNA and mRNA from the ribosome, and the splitting of the ribosome into two subunits . EF2 is folded into five domains, with domains I and II forming the N-terminal block, domains IV and V forming the C-terminal block, and domain III providing the covalently-linked flexible connection between the two. Domains III and V have the same fold (although they are not completely superimposable and domain III lacks some of the superfamily characteristics), consisting of an α/β sandwich with an antiparallel β-sheet in a (β/α/β)x2 topology . This double split β/α/β fold is also seen in a number of ribonucleotide binding proteins. It is the most common motif occurring in the translation system and is referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.
PKHD-type hydroxylase C-terminal domain (PKHD_C)
Type: Domain

This is the C-terminal domain found in PKHD-type hydroxylase enzymes. Family members are found mostly in bacteria and carry the 2OG-Fe(II) oxygenase domain (

).
Rv2175c, C-terminal (Rv2175c_C)
Type: Domain

This is the C-terminal domain of unknown function found in actinomycetes such as M. tuberculosis Rv2175c. Rv2175c has a DNA binding activity and possesses a winged helix-turn-helix fold, furthermore it is identified as a substrate of the PknL kinase .
Fatty acid synthase subunit beta, N-terminal domain (FAS1_N)
Type: Domain

This entry represents the N-terminal domain found in fatty acid synthase proteins such as

.
T-Q ester bond containing domain (TQ)
Type: Domain

This domain is found in Gram-positive bacterial surface proteins. It contains a very unusual ester bond between a conserved threonine residue on the N-terminal β-strand of the Ig-like fold and and a glutamine residue in the final strand of the domain .
Transport inhibitor response 1 domain (Transp_inhibit)
Type: Domain

The F-box protein transport inhibitor response 1 (TIR1) is a receptor for auxin, triggering an auxin-enhanced and ubiquitin-mediated degradation of substrates . The targets are recruited via interaction with the leucine-rich repeat region of the protein. This entry represents a specific unit of the LRR region, including an insertion of one short α-helix in the loop between the β-strand and the following helix. It shares some sequence homology with a unit with similar structure of coronatine-insensitive protein 1 .
UvrA, interaction domain (UvrA_inter)
Type: Domain

This domain found in UvrA proteins interacts with the UvrB protein.

In Eubacteria and some Archaea, the first steps in nucleotide excision repair are carried out by the coordinated action of the UvrA, UvrB, and UvrC proteins. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB β-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage .
Glutamate--tRNA ligase, N-terminal domain (GluRS_N)
Type: Domain

This domain is found at the N terminus of Glutamate-tRNA ligase (also known as glutamyl-tRNA synthetase) (GluRS,

). The domain adopts a classical glutathione S-transferase (GST)-like fold and it interacts with tRNA-aminoacylation cofactor ARC1 (Arc1p) N-terminal domain for the formation of aminoacyl-tRNA synthetase (aaRS) complex in yeast .
DNA processing protein A, sterile alpha motif domain (SAM_DprA)
Type: Domain

This is the N-terminal domain found in DNA processing protein A (DprA) present in Streptococcus pneumoniae. DprA has recently been discovered to be a transformation-dedicated RecA loader. Transformation is believed to play a major role in genetic plasticity. This domain is known as the sterile alpha motif (SAM) domain. DprAs are able to form a type of dimer through SAM-SAM interactions, also known as N/N interactions .
TAR DNA-binding protein 43, N-terminal (TDP-43_N)
Type: Domain

This domain can be found at the N-terminal region of transactive response DNA-binding protein 43kDa (TDP-43), an RNA transporting and processing protein whose aberrant aggregates are implicated in neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), Alzheimer's Disease, and frontotemporal dementia . TDP-43 N-terminal domain has been shown to play an important role in the aggregation of TDP-43 monomers and its loss of function affects the RNA metabolic levels . Secondary structure of the N-terminal domain consists of six β-strands and it resembles Axin 1 . This domain mediates oligomerisation .
Exoribonuclease Xrn1, D2/D3 domain (XRN1_D2_D3)
Type: Domain

This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homologue in Drosophila, known as Pacman, is required for male fertility . This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment .
RimK, preATP-grasp domain (Rimk_N)
Type: Domain

This is the N-terminal domain found in Escherichia coli RimK proteins (Ribosomal protein S6-L-glutamate ligase). This domain precedes the ATP-grasp domain .
Polyphosphate kinase, C-terminal domain 1 (PP_kinase_C_1)
Type: Domain

Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed β-sheet flanked by five α-helices. However, the structural topology and relative orientations of the helices to the β-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains .
HMW1C N-terminal (HMW1C_N)
Type: Domain

This is the N-terminal domain found in Actinobacillus pleuropneumoniae HMW1C (ApHMW1C). HMW1 adhesin is an N-linked glycoprotein that mediates adherence to respiratory epithelium through N-glycosylation of protein acceptor sites an O-glycosylation of sugar acceptor sites. The N-terminal domain forms an all alpha domain (AAD) when combined with the domain spanning from residue 154 to residue 245. The AAD interacts extensively with the C-terminal GT-B fold in order to create unique groove with potential to accommodate the acceptor protein .
Phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease 2 (PBECR2)
Type: Domain

This entry represents a predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages. The predicted active site contains a conserved arginine and threonine residues .
Pullulanase, Ins domain (Pullulanase_Ins)
Type: Domain

Pullulanases (pullulan 6-glucanohydrolase,

) are debranching enzymes that are able to hydrolyze the alpha-1,6-glycosidic linkage in pullulan, starch, amylopectin, and related oligosaccharides. Type I pullulanases specifically cleave the alpha-1,6-glycosidic linkages in pullulan and branched oligosaccharides to produce maltotriose and linear oligosaccharides, respectively . Structural analysis of Klebsiella lipoprotein pullulanase (PulA) illustrates that the catalytic core is composed of two major regions: the TIM-barrel domain A and β-sandwich fold domain C. PulA contains an extra domain, a highly mobile Ins subdomain of unknown function which is inserted into the catalytic TIM-barrel domain A of Klebsiella pullulanases. The Ins subdomain is rich in helical and loop secondary structure. A disulfide bond between Cys491 and Cys506 and two Ca2+ ions presumably stabilizes this domain. This insertion is also found in pullulanases from other Gram-negative genera that have a functional T2SS, such as Vibrio, Aeromonas, and Photorhabdus. Functional analysis indicate that this domain is required for PulA secretion via the T2SS .
Nuf2, DHR10-like domain (Nuf2_DHR10-like)
Type: Domain

This domain is found at the C-terminal region of Nuf2 proteins. This domain was identified as MazG related domain also designated as Designed helical repeat protein 10 (DHR10) that actually adopts a coiled-coil structure . Nuf2 is part of the Ndc80 complex, which complex binds to the spindle and is required for chromosome segregation and spindle checkpoint activity .
Heliorhodopsin (Heliorhodopsin)
Type: Family

Heliorhodopsins, distantly related to type-1 rhodopsins, are embedded in the membrane with their N termini facing the cell cytoplasm, an orientation that is opposite to that of type-1 or type-2 rhodopsins. Heliorhodopsins show photocycles that are longer than one second, which is suggestive of light-sensory activity. Heliorhodopsin photocycles accompany retinal isomerization and proton transfer, as in type-1 and type-2 rhodopsins, but protons are never released from the protein .
Nitrous oxide reductase, propeller repeat 1 (Nos_propeller)
Type: Repeat

Nitrous oxide reductases usually contain a seven-bladed β-propeller domain with external short α-helices . This entry represents a single blade of the propeller, with imperfect α-helix, usually at the C terminus of the repeat region.
SMODS and SLOG-associating 2TM effector domain 5 (SLATT_5)
Type: Domain

The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family contains an additional C-terminal α-helix, and strictly associates with a reverse transcriptase domain, part of a predicted retroelement with diversity-generating potential .
SMODS and SLOG-associating 2TM effector domain 3 (SLATT_3)
Type: Domain

The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT domain is always N-terminally fused to the SLATT_1 (

), and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels .
SoxA, A3 domain (SoxA_A3)
Type: Domain

This entry represents the sarcosine oxidase's alpha, A3 domain . This domain binds to FMN in sarcosine oxidase. This domain is related to the BFD-like [2Fe-2S]-binding domain (

) but lacks its iron binding cysteine residues.
Disease resistance, N-terminal (Rx_N)
Type: Domain

This entry represents the N-terminal domain found in many plant resistance proteins . This domain has been predicted to be a coiled-coil, however the structure shows that it adopts a four helical bundle fold .
SMODS and SLOG-associating 2TM effector domain 6 (SLATT_6)
Type: Domain

The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT domain associates with a SMODS nucleotide synthetase domain fused to the predicted AGS-C sensor domain. It is sometimes further coupled to R-M systems .
VapC9 PIN-like domain (PIN_9)
Type: Domain

This is a domain of unknown function that resembles the PIN-like domains. Proteins with this domain include ribonuclease VapC4 and VapC9 .
SDH, C-terminal (SDH_C)
Type: Domain

This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found just after the C-terminal domain (

) which is responsible for NADP binding .
RecJ, OB domain (RecJ_OB)
Type: Domain

This OB-fold is found in RecJ proteins where it binds to ssDNA .
Chromosome region maintenance repeat (CRM1_repeat)
Type: Repeat

Chromosome region maintenance 1 or exportin 1 mediates the nuclear transport of proteins bearing a leucin-rich nuclear export signal (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them . N-terminal, C-terminal and central repeats show slightly different structural arrangements, with N- and C- termini repeats interacting with each other. This entry represents the central repeats of CRM1.
Sensor histidine kinase (AbfS), sensor domain (AbfS_sensor)
Type: Domain

This is the sensor domain of sensor histidine kinase (AbfS) present in Cellvibrio japonicus. AbfS forms part of the AbfR/S two-component system which is needed to to activate the expression of the suite of enzymes that remove the numerous side chains from xylan. The overall fold of the sensor domain is that of a classical Per Arndt Sim domain . This domain binds xylotriose and xylobiose (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
4-hydroxyphenylacetate decarboxylase small gamma subunit, N-terminal (4HPAD_g_N)
Type: Domain

4-Hydroxyphenylacetate decarboxylase (4-HPAD) is a heterotetramer consisting of catalytic beta-subunit harboring the putative glycyl/thiyl dyad and a distinct small gamma-subunit with two [4Fe-4S] clusters (

). The gamma-subunit is proposed to be involved in the regulation of the oligomeric state and catalytic activity of the enzyme and it comprises two domains with some amino acid sequence identity that are structurally related by a pseudo-2-fold symmetry indicating a gene duplication origin. This entry represents the N-terminal domain which binds one [4Fe-4S] cluster through His3, Cys6, Cys19, and Cys36 .
Chlamydial protease/proteasome-like activity factor, PDZ domain (CPAF_PDZ)
Type: Domain

This entry represents a PDZ domain that is found in the CPAF protein from Chlamydia trachomatis .
PET hydrolase/cutinase-like (PET_hydrolase/cutinase-like)
Type: Domain

This entry includes Poly(ethylene terephthalate) hydrolase which is involved in the degradation and assimilation of the plastic poly(ethylene terephthalate) (PET) . It also includes cutinases which catalyse the hydrolysis of cutin, a polyester that forms the structure of plant cuticle . They show esterase activity towards p-nitrophenol-linked aliphatic esters (pNP-aliphatic esters) . These proteins share a PET hydrolase fold similar to that found in chlorophyllases.
Arginine decarboxylase, C-terminal helical (Arg_decarbox_C)
Type: Domain

This small three helical domain is found at the C terminus of the arginine decarboxylase enzyme .
CdiI immunity protein (CdiI_2)
Type: Domain

Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighbouring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Structure analysis of CdiI immunity protein from Yersinia kristensenii shows that it is composed of eight α-helices packed together to form a nearly spherical structure with weak structural homology to a putative TetR family transcriptional repressor. The CdiI protein fits into the curved cavity of the CdiA-CTYkris toxin domain where it most likely neutralizes toxin activity by blocking access to RNA substrates . This domain is mostly found in gammaproteobacteria.
Phage MuF, C-terminal domain (MuF_C)
Type: Domain

This entry represents a predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements and also fused to the MuF domain, a structural component of the phage head. The predicted active site contains a conserved histidine and serine residues .
Domain of unknown function DUF5624 (DUF5624)
Type: Domain

This is a domain of unknown function found mainly in bacteria.
Major vault protein repeat domain 2 (Vault_2)
Type: Domain

This short domain is found repeated numerous times in the Major vault protein.
Nucleotide modification associated domain 3 (Nmad3)
Type: Domain

This entry represents an α+β fold domain with a high conserved HxD and D motifs suggestive of enzymatic function and predicted to be involved in modifed nucleotide biosynthesis .
Major vault protein repeat domain 4 (Vault_4)
Type: Domain

This domain is found in the major vault protein.

The major vault protein is the major polypeptide component of a large cellular ribonuclear protein complex found in the cytoplasm of eukaryotic cells (known as vaults). Several roles for vaults have been proposed. Vault proteins have been associated with development of multi-drug resistance . They have also being implicated in the regulation of several cellular processes including transport mechanisms, signal transmission and immune responses .
Zinc transporter ZIP4, N-terminal (ZIP4_N)
Type: Domain

This domain is found at the N terminus of the ZRT1-IRT1-like protein 4 (ZIP4) from mammals. ZIP4 is a zinc transporter that plays an important role in cellular zinc homeostasis . This domain can also be found in ZIP12.
Major vault protein repeat domain (MVP_rep_dom)
Type: Domain

The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function . This entry corresponds to a repeated domain found in the amino terminal half of the major vault protein.
Defence against restriction A, N-terminal (DarA_N)
Type: Domain

This entry represents the N-terminal domain of the phage P1 DarA protein, which is a internal capsid protein probably ejected along with the viral DNA and prevents degradation of viral DNA by the host type I restriction-modification antiviral defense system . This α and β fold domain contains a conserved aspartate, and an asparagine residue followed by a basic residue in a Nx+ motif . This domain can also be found in the phage P1 hdf protein, a solo version of the domain. The hdf protein is also a component of the phage P1 head . The domain might be involved in a counter-restriction activity .
Diiron non-heme beta-hydroxylase, N-terminal domain (CmlA_N)
Type: Domain

This is the N-terminal domain found in Diiron non-heme beta-hydroxylase (CmlA). CmlA catalyzes beta-hydroxylation of the precursor molecule l-p-aminophenylalanine (l-PAPA) to form l-p-aminophenylserine. Structural analysis indicate that the N-terminal domain facilitates dimerization and has a mixed α-β topology. Furthermore, a projecting 'dimerization arm' (residues 108-146) from the N-terminal domain of CmlA mediates the interaction between the monomers .
Nitrous oxide reductase, propeller repeat 2 (NOS_propeller_2)
Type: Repeat

Nitrous oxide reductases usually contain a seven-bladed β-propeller domain with external short α-helices . This entry represents a single blade of the propeller, without α-helical insertion.
YgxA-like, helix-turn-helix domain (YgxA_HTH)
Type: Domain

This helix turn helix domain can be found in YgxA from Bacillus subtilis.
Stomatal closure-related actin-binding protein, PH domain (SCAB-PH)
Type: Domain

This entry is a PH domain found on plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilise actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C terminus. This domain adopts the PH fold, of seven β-strands,β7-β13 and two α-helices, α1 and α2 arranged into a β-barrel. The canonical phosphoinositide-binding pocket of the classic PH domain is degenerate in this fused one, and the charge on the pocket suggest that the Ig-PH domain contains a non-canonical binding site for inositol phosphates .
Domain of unknown function DUF5619 (DUF5619)
Type: Domain

This is a domain of unknown function found in bacteria and archaea. It adopts α/β fold composed of a central mixed β-sheet and two helices packed on both sides of the sheet

.