SII-SWORD/CoKE huggingface dataset:
DUF465 superfamily (DUF465_sf)
Type: Homologous_superfamily

Family members are found in small bacterial proteins, and also in the heavy chains of fungal proteins that contain the domain kinesin, in which this region is located C-terminal of the motor domain. Members of this family may form coiled coil structures .
Neutral ceramidase, C-terminal domain superfamily (NCDase_C_sf)
Type: Homologous_superfamily

Ceramidases play a key role in sphingolipid metabolism by converting the apoptosis-associated lipid ceramide to Sph, a precursor for the proliferative factor S1P. Three families of CDases (acid, neutral, and alkaline) have been identified that are distinguished by their pH optima, subcellular localisation, primary structure, mechanism, and function .

This superfamily represents the C-terminal domain of a group of neutral ceramidases found in both bacteria and eukaryotes . The EC classification is

. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This C-terminal tail of the enzyme is highly conserved across all species and may play a role in the interaction of the enzyme with the plasma membranes. The tail is also vital for the stabilisation of the enzyme as a whole .
CEBP, ZZ domain superfamily (CEBP_ZZ_sf)
Type: Homologous_superfamily

This entry represents the ZZ-type zinc finger domain found in the cytoplasmic polyadenylation element-binding protein. It binds zinc via two conserved histidines in the C-terminal part of the domain .
PSRP-3/Ycf65 superfamily (PSRP-3/Ycf65_sf)
Type: Homologous_superfamily

In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65, with both also known as small ribosomal subunit protein cS23. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA .
Effector protein HopAB, E3 ubiquitin ligase domain superfamily (HopAB_E3_ubiquit_lig_sf)
Type: Homologous_superfamily

HopAB family members are type III effector proteins that are secreted by the plant pathogen Pseudomonas syringae into the host plant to inhibit its immune system and facilitate the spread of the pathogen . AvrPtoB, also called HopAB3, is the best studied member of the family. It suppresses host basal defenses by interfering with PAMP (pathogen-associated molecular signature)-triggered immunity (PTI) through binding and inhibiting BAK1, a kinase which serves to activate defense signaling . It also recognizes the kinase Pto to activate effector-triggered immunity (ETI) .

AvrPtoB contains an N-terminal region that contains two kinase-interacting domains (KID) and a C-terminal E3 ligase domain. The first KID recognizes the PTI-associated kinase Bti9 as well as Pto, and is referred to as the Pto-binding domain (PID). The second KID interacts with BAK1 and FLS2, which are leucine-rich repeat-containing receptor-like kinases, and is called the BAK1-interacting domain (BID)
. The family member HopPmaL is shorter and lacks the C-terminal E3 ligase domain .

The E3 ubiquitin ligase domain found in the bacterial protein AvrPtoB inhibits immunity-associated programmed cell death (PCD) when translocated into plant cells, probably by recruiting E2 enzymes and transferring ubiquitin molecules to cellular proteins involved in regulation of PCD and targeting them for degradation. The structure reveals a globular fold centred on a four-stranded β-sheet that packs against two helices on one face and has three very extended loops connecting the elements of secondary structure, with remarkable homology to the RING-finger and U-box families of proteins involved in ubiquitin ligase complexes in eukaryotes .
SirA superfamily (SirA_sf)
Type: Homologous_superfamily

This entry includes the sporulation inhibitor of replication (sirA) protein from Bacillus subtilis and related proteins. SirA is a DnaA-interacting protein that inhibits initiation of replication in diploid Bacillus sp. cells committed to the developmental pathway leading to formation of a dormant spore. SirA protein synthesis is induced by the response regulator Spo0A, the master regulator for entry into sporulation .
Photosystem II Psb27 superfamily (PSII_Psb27_sf)
Type: Homologous_superfamily

This entry represents Psb27, a small thylakoid lumen-localised protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex . Psb27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminal .
Arterivirus nsp7 alpha superfamily (Arteri_nsp7a_sf)
Type: Homologous_superfamily

Translation of the arterivirus genome results in two large precursor polyproteins, pp1a and the C-terminally extended frameshift product pp1ab. These proteins are cleaved by up to four virus-encoded proteases to yield at least 13 nonstructural proteins (nsps) (nsp1 to nsp12, including nsp7) plus a substantial number of processing intermediates of unknown function. Nsp7 can be internally cleaved by the nsp4 protease, yielding small amounts of nsp7alpha and nsp7beta. This entry represents nsp7alpha, which is likely to have a role in viral RNA synthesis .
Channel forming colicin, central receptor recognition domain superfamily (Channel_colicin_cen_sf)
Type: Homologous_superfamily

Colicins are plasmid-encoded polypeptide toxins produced by and active against Escherichia coli and closely related bacteria. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis.

Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy . These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane .

This entry represents the central receptor recognition domain, which has an α/β two-layer sandwich structure.
DUF3220 superfamily (DUF3220_sf)
Type: Homologous_superfamily

This superfamily represents a domain of unknown function which appears to be restricted to Bordetella proteins. This domain consists of 3 α helices.
DnaA, N-terminal domain superfamily (DnaA_N_sf)
Type: Homologous_superfamily

This entry represents the N-terminal domain of bacterial DnaA proteins , which play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). The structure of this domain is known . Its exact function is uncertain, but it has been suggested that the domain may play a role in oligomerisation.
Mite allergen, group 5/21 superfamily (Mite_allergen_group-5/21_sf)
Type: Homologous_superfamily

This entry contains mite allergens Der p 5 and Blo t 5 , belonging to the mite group 5 allergen family, Blo t 21 and Der f 21 belonging to group 21. Mite allergens causes an allergic reaction in humans . Common symptoms of mite allergy are bronchial asthma, allergic rhinitis and conjunctivitis. Der p 5 binds to IgE.
Macin superfamily (Macin_sf)
Type: Homologous_superfamily

The macin superfamily consists of theromacin, neuromacin and hydramacin-1. All of the macins exert antimicrobial activity , but neuromacin also possesses nerve repair activity . Structurally, they form a disulphide-stabilised α-β motif .
3-mercaptopyruvate sulfurtransferase, C-terminal domain superfamily (SulfurTase_C_sf)
Type: Homologous_superfamily

This entry represents a domain found in putative 3-mercaptopyruvate sulphurtransferases from Trypanosomatida (kinetoplastids). Leishmania major 3-mercaptopyruvate sulfurtransferase consists of a crescent-shaped molecule comprising three domains. The N-terminal and central domains are similar to the thiosulfate sulfurtransferase rhodanese domain. The 80-amino acid C-terminal domain adopts a structure consisting of a four-stranded antiparallel β-sheet and an α-helix, arranged in a β(2)-α-β(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase . The C-terminal domain may be involved in mediating protein folding and sulfurtransferase-protein interactions .
NADH-quinone oxidoreductase, subunit 15 superfamily (NADH_quinone_OxRdtase_su15_sf)
Type: Homologous_superfamily

This entry represents subunit 15 of NADH-quinone oxidoreductase, also known as Complex I. The nqo15 subunit has probably a role in complex stabilisation, and may be also involved in the storage of iron for iron-sulphur cluster regeneration in the complex .
tRNA methyltransferase TRM10-type domain superfamily (MT_TRM10-typ_sf)
Type: Homologous_superfamily

This entry represents a domain found in class IV SAM-dependent methyltransferases TRM10-type . Methyltransferases classified as class IV (SPOUT) are homodimers and methylate only RNA. The common core of the SPOUT fold contains a five-stranded β-sheet, flanked by two layers of α-helices. The core can be divided into two subdomains, both displaying an α/β architecture: (1) the N-terminal strands exhibit a Rossmanoidal α/β fold while (2) an important part of the C-terminal (~ 30 residues) is tucked back into the structure forming a conserved topological trefoil knot where SAM binding occurs. The active site, located at the interface of the two subunits, is
formed by amino acids from both monomers .

TRM10-type methyltransferases include tRNA (guanine(9)-N(1))-methyltransferase, tRNA (adenine(9)-N(1))-methyltransferase and RNA (guanine-9-)-methyltransferase domain-containing protein. TRM10 homologues are widely found in eukaryotes and archaea, but not in bacteria.
Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily (AcetylCoA_hyd_C_sf)
Type: Homologous_superfamily

This entry represents an acetyl-CoA hydrolase/transferase C-terminal domain.
This domain is found in several enzymes which take part in pathways involving acetyl-CoA, including acetyl-CoA hydrolase, succinyl-CoA:coenzyme A transferase (CAT1), propionyl-CoA:succinate CoA transferase, and 4-hydroxybutyrate coenzyme A transferase (CAT2).
Schlafen, AlbA_2 domain superfamily (Schlafen_AlbA_2_dom_sf)
Type: Homologous_superfamily

This entry represents the AlbA clan of DNA-binding domains.
YaiA-like superfamily (YaiA-like_sf)
Type: Homologous_superfamily

This superfamily of proteins is found in Enterobacteriaceae, where they are immediately downstream of a Shikimate kinase.
CedA-like superfamily (CedA-like_sf)
Type: Homologous_superfamily

CedA is involved in the regulation of cell division in Escherichia coli and related organisms. It is structurally similar to dsDNA-binding domains and has been found to interact with dsDNA. The protein comprises four antiparallel β-strands, an α-helix, and a large unstructured N terminus. As dsDNA binding domains, it may also bind dsDNA by inserting the β-sheet into the major groove of the DNA .
Large ribosomal subunit protein eL38 superfamily (Ribosomal_eL38_sf)
Type: Homologous_superfamily

Ribosomal protein eL38 forms part of the 60S ribosomal subunit .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
APS reductase, beta subunit, C-terminal domain superfamily (APS_reduc_Bsu_C_sf)
Type: Homologous_superfamily

During dissimilatory sulphate reduction and sulphur oxidation, adenylylsulphate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulphite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. This entry describes the C-terminal domain of the beta subunit of APS reductase. The C-terminal segment of the beta-subunit wraps around the alpha-subunit to form a functional unit, with the C-terminal loop inserted into the active-site channel of the alpha-subunit from another alphabeta-heterodimer .
Peptidase S8, pro-domain superfamily (S8_pro-domain_sf)
Type: Homologous_superfamily

This domain is the pro-domain found at the C terminus of several peptidases belonging to family S8 . The overall fold of the PC1 pro-domain consists of two α-helices and four β-strands in a β-α-β-β-α-β arrangement.
Peptide chain release factor 3, domain III superfamily (RF3_dom_3_sf)
Type: Homologous_superfamily

This entry represents the C-terminal domain (domain III) of peptide chain release factor 3 (RF3), a bacterial class 2 release factor . TRF3 is believed to have a role in dissociating the class 1 release factors from the ribosome following termination.
Transport accessory protein MmpS, C-terminal (MmpS_C)
Type: Homologous_superfamily

This superfamily represents the C-terminal soluble domain characterised in MmpS4 from Mycobacterium tuberculosis, but is also present in other transport accessory proteins, including MmpS1-5 from Mycobacterium tuberculosis . They are part of an export system required for biosynthesis and secretion of siderophores, and are essential for virulence of Mycobacterium tuberculosis . MmpS4 possesses an N-terminal transmembrane (TM) helix and a C-terminal soluble domain .
tRNAHis guanylyltransferase Thg1 superfamily (tRNAHis_GuaTrfase_Thg1_sf)
Type: Homologous_superfamily

tRNA His molecules are unusual in having an extra 5' GMP residue (G(-1)) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G(-1) residue is a rare example of nucleotide addition occurring at an RNA 5' end in a normal phosphodiester linkage. In Saccharomyces cerevisiae, YGR024c (Thg1p) protein is responsible for this guanylyltransferase reaction . It catalyses the guanylyltransferase step of G(-1) addition using a ppp-tRNA His substrate, and appears to catalyse the activation step using p-tRNA His and ATP. Thus, it catalyses phosphodiester bond formation at the 5' end of RNAs, formally in a 3'-5' direction .
Cellulose synthase subunit D superfamily (Cellsynth_D_sf)
Type: Homologous_superfamily

Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium spp. More correctly designated as "cellulose synthase catalytic subunits", plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity .

An operon encoding 4 proteins required for bacterial cellulose biosynthesis (bcs) in Acetobacter xylinus (Gluconacetobacter xylinus) has been isolated via genetic complementation with strains lacking cellulose synthase activity . Nucleotide sequence analysis showed the cellulose synthase operon to consist of 4 genes, designated bcsA, bcsB, bcsC and bcsD, all of which are required for maximal bacterial cellulose synthesis in A. xylinum.

The calculated molecular mass of the protein encoded by bcsD is 17.3kDa . The function of BcsD is unknown.
MecA, C-terminal domain superfamily (MecA_C_sf)
Type: Homologous_superfamily

MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. It acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, it inhibits sporulation. It is also involved in Spx degradation by ClpC .

This entry represents the C terminus region of MecA.
DNA sulphur modification protein DndE superfamily (DndE_sf)
Type: Homologous_superfamily

This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA (phosphorothioation). The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is part of a protein complex that also includes IscS, DndC, and DndE, involved in phosphorothioation (PT) . DndE binds to DNA in vitro, with a preference for nicked dsDNA , but its nicked dsDNA-binding capacity does not seem essential for PT modification .
VirC2, C-terminal domain superfamily (VirC2_C_sf)
Type: Homologous_superfamily

VirC2 is known to be involved in virulence in Agrobacterium species but its exact function is unclear . This entry represents the C-terminal domain of VirC2. This is a domain with a ribbon-helix-helix core topology consisting of four helices in an open array of two hairpins.
Polyketide synthesis cyclase superfamily (Polyketide_synth_cyclase_sf)
Type: Homologous_superfamily

Aromatic polyketides are assembled by a type II (iterative) polyketide synthases (PKSs) in bacteria. Type II PKS complexes consist of several monofunctional or bifunctional proteins which produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclization pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits .

This superfamily represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.

Tetracenomycin F2 cyclase (TcmI) catalyses an aromatic rearrangement in the biosynthetic pathaway of tetracenomycin C from Streptomyces glaucescens. The protein is a homodimer where each subunit forms a β-α-β fold belonging to the ferrodoxin fold superfamily . Four strands of antiparallel sheets and a layer of α helices create a cavity which was proposed to be the active site. This structure shows strong topological similarity to a polyketide monoxygenase (

) from S. coelicolor which functions in the actinorhodin biosynthesic pathway . It was suggested, therefore, that this fold is well suited to serve as a framework for rearrangements and chemical modification of polyaromatic substrates.
RecG, C-terminal domain superfamily (RecG_C_sf)
Type: Homologous_superfamily

This domain is found in the C-terminal section of the ATP-dependent DNA helicase RecG. It may interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. The domain is also found in a number of other proteins, many of which are putative transcriptional regulators.
UvrC, RNAse H endonuclease domain superfamily (UvrC_RNase_H_dom_sf)
Type: Homologous_superfamily

Nucleotide excision repair (NER) is a conserved DNA repair pathway that enables the repair of chemically and structurally distinct DNA lesions. In prokaryotes, the UvrA, UvrB and UvrC proteins mediate NER in a multistep, ATP-dependent reaction. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. UvrC proteins contain conserved regions: the GIY-YIG domain, the cys-rich region, the UvrBC domain which interacts with uvrB, the RNAse H endonuclease domain and the Helix hairpin Helix (HhH)2 domain .

This entry represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteristic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates .
Arylsulfotransferase, N-terminal domain superfamily (ASST_N_sf)
Type: Homologous_superfamily

This entry represents the small N-terminal domain found in arylsulfotransferases. Arylsulphotransferase (ASST) transfers a sulphate group from phenolic sulphate esters to a phenolic acceptor substrate . Each ASST monomer consists of a small, N-terminal 7-stranded β-sandwich domain, and a large C-terminal, 6-bladed β-propeller domain .
Fimbrillin subunit EcpA superfamily (Fimbrillin_EcpA_sf)
Type: Homologous_superfamily

This superfamily represents the fimbrillin protein MatB . It is also known as EcpA, and is part of the ecpRABCDE operon, which encodes the E.coli common pilus (ECP), an adhesive structure produced by all E. coli pathogroups and plays a dual role in early-stage biofilm development and host cell recognition .
Transthyretin-like superfamily (Transthyretin-like_sf)
Type: Homologous_superfamily

A series of nematode-specific transthyretin-like proteins have being identified, including transthyretin-like protein TTR-52. TTR-52 mediates recognition of apoptotic cells by the phagocyte receptor CED-1 . The function of the others remains unknown.
YuaB-like superfamily (YuaB-like_sf)
Type: Homologous_superfamily

BslA (YuaB) is a protein from Bacillus subtilis acting as a hydrophobin, which forms surface layers around biofilms and participates in biofilm assembly. BslA consists of an Ig-type fold with the addition of an unusual, extremely hydrophobic 'cap' region. The cap structure is essential for its activity and for the ability of bacteria to form hydrophobic, non-wetting biofilms . A number of domains in various proteins from Bacilli and other bacterial lineages appear related to BslA, but do not conserve the hydrophobic cap.