SII-SWORD/CoKE huggingface dataset:
NADH-ubiquinone oxidoreductase, ferredoxin-like domain (NADH_UbQ_OxRdtase_ferredoxin)
Type: Domain

This entry represents the second ferredoxin-like domain found in proteins from the complex I 75 kDa subunit family, including human NADH-ubiquinone oxidoreductase 75 kDa subunit , mitochondrial , NADH-quinone oxidoreductase subunit G from Escherichia coli and NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial from Arabidopsis thaliana . This domain contains a Fe4-S4 cluster, one of the redox centres of the complex . This domain is also found in related proteins such as NAD-reducing hydrogenase HoxS subunit gamma that along with subunit alpha exhibits NADH:oxidoreductase activity . It is also found in the NADP(+)-dependent formate dehydrogenase subunit alpha which is involved in the NADP-dependent reduction of CO2 to format .
Aspartokinase, ACT domain (ACT_Aspartokinase)
Type: Domain

This entry represents the ACT domain, found in Aspartate kinases from bacteria, archaea, plants and fungi. Aspartate kinase catalyses the phosphorylation of aspartic acid . Some members of this entry are bifunctional aspartokinase/homoserine dehydrogenases. This domain folds as a four-stranded antiparallel sheet with two α-helices parallel to the sheet and located on one side of the sheet .
Transposase for insertion sequence element IS21-like, C-terminal domain (IstA-like_C)
Type: Domain

This entry represents a domain found towards the C-terminal end of Transposase for insertion sequence element IS21 from Pseudomonas aeruginosa (IstA) and similar prokaryotic integrases and transposases. This region adopts a β-barrel structure with Greek-key topology .
Dynein 2 heavy chain 1, cytoplasmic, ATPase lid domain (DYNC2H1-like_lid)
Type: Domain

Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head with six AAA-domains, a coiled-coil stalk with a microtubule binding domain (MTBD) and a linker .

This entry represents the lid domain found at the C-terminal of the third AAA+ ATPase domain in human Cytoplasmic dynein 2 heavy chain 1 (DYNC2H1) and similar eukaryotic sequences .
Decaheme cytochrome c component MtrF-like, domain III (MtrF-like_dom_III)
Type: Domain

This entry represents domain III of the decaheme cytochrome c component MtrF and similar proteins. MtrF is part of the MtrFDE complex and is a homologue of MtrC. In Shewanella oneidensis, these proteins are located at bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilisation of extracellular mineral forms of iron and manganese as respiratory electron acceptors . MtrC/MtrF consist of four domains: domain I and III containing seven antiparallel β-strands in an extended Greek key topology; domains II and IV each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core (

), flanked by domains I (

) and III .
Peptidoglycan muramidase Tse3, N-terminal domain (Tse3_N)
Type: Domain

This entry represents the catalytic domain found in Peptidoglycan muramidase Tse3. Tse3 is a toxin secreted by the H1 type VI (H1-T6SS) secretion system into the periplasm of recipient cells. This protein degrades peptidoglycan via muramidase activity. Tse3 is composed of a small N-terminal domain, which contains seven α-helices packed in a rod-like helical repeat motif, and a C-terminal catalytic domain (

) .
Peroxisomal multifunctional enzyme type 2-like, N-terminal domain (MFE-2_N)
Type: Domain

This entry represents a domain found at the N-terminal of Peroxisomal multifunctional enzyme type 2 (also known as MFE-2 hydratase 2) and related enzymes . This domain is housing the cavity for the aliphatic acyl part of the substrate molecule. The flexibility of region within this domain plays a role in substrate binding in mammalian hydratase 2 .
Magnetotaxis protein MtxA, C-terminal domain (MtxA_C)
Type: Domain

This domain is found at the C-terminal end of Magnetotaxis protein MtxA from Magnetospirillum gryphiswaldense (

) and similar sequences from magnetotactic aquatic proteobacteria. Magnetotaxis is believed to direct the swimming of cells toward growth-favoring microoxic zones in natural waters. This domain contains five anti-parallel α-helices-and-turn motifs folded as tetra-trico-peptide repeat (TPR) motifs .
Magnetotaxis protein MtxA, middle immunoglobulin-like domain (MtxA_M_Ig-like)
Type: Domain

This immunoglobulin-like domain is located centrally in the Magnetotaxis protein MtxA from Magnetospirillum gryphiswaldense (

) and similar sequences from magnetotactic aquatic proteobacteria. Magnetotaxis is believed to direct the swimming of cells toward growth-favoring microoxic zones in natural waters .
Internalin K, domain D2 (InlK_D2)
Type: Domain

This entry represents domain D2 of the surface-associated internalin InlK from Listeria monocytogenes (

), also present in similar proteins mainly found in Bacilli. InlK interacts with the highly conserved major vault protein (MVP), the main component of cytoplasmic ribonucleoproteic particules named vaults that are widely expressed in all eukaryotic organisms. Thus, it plays a key role in the listerial infection process . In the structure of this protein, this domain is located at the elbow and has a β-sandwich-like fold .
Zinc finger CCCH domain-containing protein 4/6/8, CCCH zinc finger (Znf-CCCH_ZC3H4/6/8)
Type: Domain

This domain is found in human KIAA1064 (also known as Zinc finger CCCH domain-containing protein 4), Zinc finger CCCH domain-containing protein 6 and 8. ZC3H4 is a RNA-binding protein that suppresses transcription of long non-coding RNAs (lncRNAs) . ZC3H8 is a component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III .
Exuperantia RNAse H-like domain (Exu_RNase_H-like)
Type: Domain

This entry represents the RNAse H-like domain found at the N-terminal of exuperantia (Exu) from Drosophila and similar sequences from insects. Exu is a RNA-binding pseudonuclease associated with bicoid mRNA and required for its localisation . The catalytic site is degenerate and inactive, and as such, this domain mediates dimerisation and RNA binding.
Glycosyl hydrolase family 95, catalytic domain (GH95_cat)
Type: Domain

This entry represents the central catalytic domain of proteins from the GH95 family of glycosyl hydrolases, including Alpha-1,2-fucosidase 2 from Arabidopsis thaliana, which catalyses the hydrolysis of an alpha-1,2-linked fucose . A member of this family, FucOB from A. muciniphila was shown to hydrolyse all three types of H antigen structures to obtain the afucosylated Bombay phenotype . This domain shows an (α/α)6 helical barrel topology.
Ca3427-like, PBP 2 (Ca3427-like_PBP2)
Type: Domain

This entry represents domain II of CA3427 from Candida albicans (

), which consists of a 5 stranded β-sheet . Members of this group are found in fungi and bacteria.
Lreu_0056-like (Lreu_0056-like)
Type: Domain

This entry represents a domain found in a family of uncharacterised Lactobacillus proteins. The structure of a family member, a hypothetical protein Lreu_0056 from Lactobacillus reuteri (

), adopts an α+β structure in order α(2)-β(5)-α(2) consisting of a five-stranded antiparallel β-sheet with helices packed on one side of the sheet (

).
RepB/MobA-like, C-terminal domain (RepB/MobA-like_C)
Type: Domain

This entry represents a domain found at the C-terminal of DNA primase from Acidithiobacillus ferrooxidans (RepB), Mobilization protein A from Escherichia coli (MobA) and similar sequences mainly found in proteobacteria. This domain adopts a helical configuration .

RepB is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long α-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication. RepBprime primases recognise both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesise primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode .

MobA is part of the relaxosome complex that is responsible for plasmid transfer during conjugation. It unwinds DNA and catalyses the cleavage of one of the DNA strands at oriT. The cleaved strand is then transferred through the dedicated type IV secretion apparatus. The primase activity of MobA is essential for the synthesis of primers that will initiate the DNA replication events necessary to form the double-stranded plasmid in the recipient cell .
Oxo-glucose-6-phosphate:glutamate aminotransferase, N-terminal domain (NtdA_N)
Type: Domain

This entry represents the N-terminal domain of 3-oxo-glucose-6-phosphate:glutamate aminotransferase from Bacillus subtilis (NtdA), which is not found in other aminotransferases and consists of two-stranded parallel β-sheet flanked by two α-helices . This domain may be involved in protein-protein interactions. NtdA is a sugar aminotransferase involved in the biosynthesis of kanosamine(3-amino-3-deoxy-D-glucose), which is known to have antibiotic and antifungal properties, and to be a precursor of the antibiotic neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose (NTD)) . Members of this group are specific to Bacillales.
Alp7A-like, C-terminal domain (Alp7A-like_C)
Type: Domain

Bacterial Actin-Like Proteins (ALPs) participate in many biologically, clinically and commercially important processes, including segregation of low-copy plasmids. Alp7A is a bacterial actin that functions in plasmid segregation. It is composed of two domains both structurally similar to domains of actin-like ATPases (

). This entry represents the C-terminal domain.
CRISPR-associated endonuclease Cas9, wedge domain (Cas9_WED)
Type: Domain

In the type II CRISPR-Cas system, the Cas9 effector nuclease associates with dual guide RNAs (crRNA and trans-activating crRNA (tracrRNA)) and cleaves double-stranded DNA targets complementary to the crRNA guide. Cas9 is composed of multiple domains. This entry represents the so-called wedge (WED) domain that is found in Campylobacter jejuni CRISPR-associated endonuclease Cas9, one of the smallest Cas9 orthologues, and similar proteins specific to Campylobacterales. The WED domain is involved in the recognition of PAM-containing duplex formed by the target and non-target DNA strands. It consists of a β-hairpin packed with two short α-helices (

) .
T4SS protein CagL-like (CagL-like)
Type: Family

This family includes CagL from Helicobacter pylori (

), a type IV secretion system (T4SS) pilus protein that interacts with several integrins through an helical RGD motif. It shows an all-α structure that undergoes specific conformational changes depending on pH variations. These changes also affect the exposure of the RGD motif and therefore modulate its binding capacity to host cell integrins .
Exosome RNA binding protein RRP4, N-terminal domain (RRP4_N)
Type: Domain

This domain is found N-terminal in exosome RNA binding protein RRP4 and related proteins from archaea . RRP4 is a part of the exosome regulatory substrate recognition platform. This domain is structurally similar to ribosomal L27 protein.
Gp38-like (Gp38-like)
Type: Family

This entry represents a family of proteins from tailed bacteriophages, including the gene product 38 (Gp38) from Lactococcus phage, a short protein consisting of 71 amino acids. It is also known as the AbiQ resistance protein due to its involvement in escaping bacterial killing mediated by the AbiQ protein. Gp38 is expressed early in the viral replication cycle and is essential for virus function .
CRISPR-associated endonuclease Cas9, PI domain, C-terminal, campylobacterales (Cas9_PI_C_campylobact)
Type: Domain

In the type II CRISPR-Cas system, the Cas9 effector nuclease associates with dual guide RNAs (crRNA and trans-activating crRNA (tracrRNA)) and cleaves double-stranded DNA targets complementary to the crRNA guide. Cas9 is composed of multiple domains.

This entry represents the C-terminal lobe of the so-called PAM-interacting (PI) domain found in Campylobacter jejuni CRISPR-associated endonuclease Cas9, one of the smallest Cas9 orthologues, and similar proteins specific to Campylobacterales. The PI domain is involved in the recognition of PAM-containing duplex formed by the target and non-target DNA strands. This domain facilitates the target DNA unwinding and the heteroduplex formation. The region represented in this entry adopts a partly open six-stranded β-barrel with a SH3-like topology (

) .
AF1548-like, C-terminal (AF1548-like_C)
Type: Domain

This domain is found at the C-terminal of the uncharacterised protein AF_1548 from Archaeoglobus fulgidus and similar prokaryotic proteins. This domain is often found associated with

.
MrkH-like, YcgR-like domain (MrkH_YcgR-like_dom)
Type: Domain

This entry represents the YcgR-like domain found at the N-terminal of MrkH (

) from Klebsiella pneumoniae and similar sequences . Some members included in this contain a PilZ domain (

) at the C-terminal. MrkH is a c-di-GMP-related transcriptional regulator that affects type 3 fimbrial expression in response to cellular c-di-GMP level, playing and important role in biofilm formation. This protein binds to the promoter regulation fragments of MrkHI and MrkA mainly through its PilZ domain and this YcgR-like domain also participates in DNA-binding .
CdsD, periplasmic PD2 domain (CdsD_PD2)
Type: Domain

This domain is found in CdsD from Chlamydia trachomatis (

) and similar sequences from Chlamydia. CdsD is a structural contact-dependent secretion (Cds) protein that form part of the basal body of the type III secretion system (T3SS) injectisome of the bacteria. The periplasmic part of this protein contains at least 3 domains: PD1, PD2 (represented in this entry) and PD3 (

), all of them sharing the same α-β-β-α-β topology, known as the BON fold, in which the two antiparallel α-helices are on the same side of a three stranded β-sheet .
tRNA(Ile)-lysidine synthase-like, C-terminal domain (TilS-like_C)
Type: Domain

This entry represents the C-terminal domain of tRNA(Ile)-lysidine synthase from Aquifex aeolicus (TilS) and similar bacterial sequences. TilS ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner . It is probably implicated in the recognition of the tRNA acceptor stem .
Type VI lipoprotein IgE-like, C-terminal domain (IgE-like_C)
Type: Domain

This entry represents the C-terminal domain of the intracellular growth locus E (IglE) protein from Francisella tularensis subsp. novicida . The lipoprotein IglE has been identified as a virulence factor that functions as a regulator of the Type IV system-mediated secretion . This domain is predicted to show a mainly β configuration.
BA_2335-like (BA_2335-like)
Type: Family

This protein family includes the uncharacterised protein BA_2335 from Bacillus anthracis and similar sequences from Bacilli. It adopts a β-sandwich configuration.
CydS-like (CydS)
Type: Family

This entry represents the CydS subunit of the cytochrome bd oxidase . This protein is very short and forms a single α-helix that is part of the complex . Members of this family are found in Bacillales.
Winged helix domain, alphaproteobacteria (wHTH_alphaproteobact)
Type: Domain

This entry represents a winged helix-turn-helix (wHTH) domain mainly found in alphaproteobacteria that is likely to be involved in DNA-binding.
PspA associated protein B-like (PspAB-like)
Type: Family

This entry represents a family of poorly characterised prokaryotic proteins, including PspA associated protein B, a component of the Psp system. It occurs in an operon with a membrane-associated metallopeptidase. In addition, these two genes occur in operon with the PspA-PspAA dyad .
SecDF, P1 head subdomain (SecDF_P1_head)
Type: Domain

This entry represents the head subdomain from P1 domain from SecDF proteins, which constitutes a critical element for proton transport . P1 domain binds an unfolded protein, and undergoes functionally important conformational changes. SecDF functions as a membrane-integrated chaperone that mediates ATP-independent protein translocation.
Anti-restriction endonuclease (Arn)
Type: Family

This entry represents Anti-restriction endonuclease from Enterobacteria phage T4 () proteins and similar sequences from tailed bacteriophages. Arn plays a role in the inhibition of the host restriction-modification system. Arn was identified as an inhibitor of the restriction enzyme McrBC. Its structure consists of a three-stranded, anti-parallel β-sheet on one side, while on the other side, four α-helices are bundled together. A structural analysis of Arn revealed that its shape and negative charge distribution are similar to dsDNA, suggesting that this protein could act as a DNA mimic .
RIM, zinc finger (RIM_Znf)
Type: Domain

This entry represents the zinc finger domain of Regulating synaptic membrane exocytosis protein 1/2 (RIM1/2) and related proteins. This domain alone is responsible for the interaction with Munc13-1 by engaging with the Munc13-1 C2A domain . Structurally, this domain is similar to FIVE zinc fingers.

RIM proteins are scaffolding proteins at the active zone which bind to several other presynaptic proteins. The long isoforms of RIM proteins, which contain N-terminal Rab3 and Munc13 interacting domains, as well as a central PDZ domain and two C-terminal C2 domains, are encoded by two genes, Rim1 and Rim2 . They have multiple isoforms (alpha, beta, gamma) diverging in their structural composition, which mediate overlapping and distinct functions . These isoforms are involved in determining Ca2+ channel density and vesicle docking at the presynaptic active zone .
Argonaute, N-terminal domain, bacteria (Ago_N_bact)
Type: Domain

This domain is found at the N-terminal bacterial Argonaute (Ago) . Ago binds small RNA or DNA guides, which provide base-pairing specificity for the recognition and cleavage of complementary nucleic acid targets. Bacterial Ago uses 5'-hydroxylated guide RNAs to recognise and cleave single-stranded target sequences rather than the 5'-phosphorylated guides used by all known Argonautes . Bacterial Ago adopts a bilobed structure; an N-terminal and a PAZ domain constitute one lobe, the second one consists of a middle (MID) domain and the catalytic PIWI domain. This N-terminal domain adopts an α/β structure consisting of four-stranded β-sheet and two helices. Compared to other Argonaute proteins, this N-terminal domain differs in both its secondary structure and its orientation relative to the MID/PIWI lobe.
T6SS, Phospholipase effector Tle1-like, C-terminal domain (Tle1-like_C)
Type: Domain

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

) and similar proteins from proteobacteria. Tle1, which hydrolyse membrane phospholipids, is organised into two distinct parts, the phospholipase catalytic module (

) and the putative membrane-anchoring module (this entry), that can be divided into three independent domains: a three α-helix bundle, a six α-helix bundle and an α/β mixed fold with a two-layer sandwich structure .
Argonaute, N-terminal domain, archaea (Ago_N_arc)
Type: Domain

Argonaute (Ago) proteins are found in all three domains of life. They share a common molecular architecture, with the C-terminal lobe consisting of the middle (Mid) and PIWI (P element wimpy testis) domains and the N-terminal lobe containing the N-terminal and PIWI-Argonaute-Zwille (PAZ) domains. Archaeal argonaute proteins are guided by 5'-phosphorylated DNA strands and exclusively process cognate DNA targets. This entry represents the N-terminal domain of the archaeal argonaute protein found in M.jannaschii. This domain consists of a four-stranded antiparallel β-sheet and an α-helix .
DNA repair helicase XPD, arch domain (XPD_arch)
Type: Domain

This domain is found in DNA repair helicase XPD from Sulfurisphaera tokodaii (

) and similar archaeal proteins. XPD, which functions as a 5'-3' DNA helicase, shows three major domains. This entry represents the central domain, called arch domain, which folds into a mixed α/β topology with a four-stranded antiparallel β-sheet and four α-helices. The other two canonical motor domains are represented by

at the N-terminal end and

at the C-terminal end .
VipD-like, C-terminal domain (VipD-like_C)
Type: Domain

This domain is found in VipD from Legionella pneumophila (effector vacuolar protein sorting inhibitor protein D,

), which localises to early endosomal membranes and alters their lipid and protein composition. This process protects the pathogen from endosomal fusion. VipD adopts a two-domain fold, with a N-terminal domain homologous to patatin (

) and a C-terminal domain (this entry) that contains ten α-helices and two short β-strands. VipD localises to early endosomes via this domain .
Thiaminase-1, insert domain (Thiaminase-1_dom)
Type: Domain

This domain is found in Thiaminase-1 from Paenibacillus thiaminolyticus and similar bacterial sequences. This enzyme degrades thiamine by replacing its thiazole moiety with a wide range of nucleophiles. This entry represents one of its two α/β-type domains, which is inserted into the other (

) .
Hydroxylamine oxidoreductase, C-terminal domain (Hao_C)
Type: Domain

This domain is found at the C-terminal end of Hydroxylamine oxidoreductase from Kuenenia stuttgartiensis (Hao,

) and similar bacterial sequences. This enzyme is responsible for the formation of NO from hydroxylamine in aerobic ammonium-oxidising bacteria. This domain shows a predominantly α-helical structure .
Capsid protein, C-terminal domain, fungal virus (P2_C_fungal_virus)
Type: Domain

This domain is found at the C-terminal end of Capsid protein from Penicillium chrysogenum virus (P2), which self-assembles to form an icosahedral capsid with a T=1 symmetry. It is organised into two domains with similar α-β topology (

) .
GtfA, extended beta-sheet meander domain (GtfA_EBD)
Type: Domain

This entry represents the extended β-sheet meander domain (EBD) of UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit and similar proteins mainly from firmicutes. GtfA is the core enzyme of the OGT complex, which also includes the co-activator GtfB, to glycosylate the serine-rich repeat (SRR) of adhesin PsrP in Streptococcus pneumoniae, a protein involved in the infection and pathogenesis . The function of this domain is not clear.
LicP, N-terminal prodomain (LicP_N_prodom)
Type: Domain

LicP is a class II LanP protease that is involved in the biosynthesis of the lantibiotic lichenicidin. This enzyme is an extracellularly located serine protease expressed by some strains of Bacillus licheniformis and undergoes a self-cleavage maturation resulting in two fragments, the N-terminal prodomain (this entry) and the C-terminal catalytic protease domain (

). The prodomain folds into a single compact domain consisting of four antiparallel β-strands interconnected with two α-helices .
AcrIC5-like domain (AcrIC5-like_dom)
Type: Domain

This entry represents a domain that covers the whole length of AcrIC5 and is found at the C-terminal end of other proteins from tailed bacteriophages and bacterial prophages.

AcrIC5 is one of the earliest discovered AcrIC proteins that inhibit type I-C CRISPR-Cas systems. AcrIC5 adopts an α/β structure consisting of a β-hairpin and three α-helices (

,

) . The presence of a highly acidic surface patch suggests that AcrIC5 might inhibit the type I-C CRISPR-Cas system by directly binding to the DNA target binding site in the system by mimicking DNA.