SII-SWORD/CoKE huggingface dataset:
CysA, C-terminal regulatory domain (CysA_C)
Type: Domain

ABC (ATP-binding cassette) transporters share a common architecture comprising two variable hydrophobic transmembrane domains (TMDs) that form the translocation pathway and two conserved hydrophilic ABC-ATPases that hydrolyze ATP. This is the C-terminal regulatory domain found at the ATPase subunit of CysA, a putative sulfate ABC transporter from Alicyclobacillus acidocaldarius. The regulatory domain of CysA is built up of an elongated β-barrel composed of two β-sandwiches that form a common hydrophobic core .
Defective in germ line development protein 3-like, KH5 domain (GLD-3-like_KH5)
Type: Domain

This entry corresponds to KH5 of Defective in germ line development protein 3 from Caenorhabditis elegans (GLD-3) and similar proteins from nematodes.

GLD-3 is required maternally for germline survival and embryogenesis. It forms a complex with Gls-1 which promotes the oogenic cell fate by freeing the translational repressor Fbf to repress sperm promoting factors. This protein promotes maturation of primary spermatocytes to mature sperm and is required during hermaphrodite development to promote sperm fate, which is critical for determining the normal number of sperm. It is also required during male development for the continued production of sperm and inhibition of oogenesis. Together with Gld-2, promotes the transition from mitosis to meiosis . GLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The four K homology (KH) domains KH2 to KH5 form a proteolytically stable structure .
Rnh202, triple barrel domain (Rnh202_N)
Type: Domain

This entry represents the N-terminal triple barrel domain found in Rnh202 (also known as ribonuclease H2 subunit B), a non catalytic subunit of ribonuclease H2. RNases H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA. It prevents genomic instability and the accumulation of aberrant nucleic acid .
Large polyvalent protein associated domain 37 (LPD37)
Type: Domain

This is and α and β fold domain that is found in polyvalent proteins that are likely to be phage/prophage-derived .
SLOG cluster3 family (LD_cluster3)
Type: Family

This entry represents a subfamily of the SLOG superfamily, observed to associate with a predicted effector protein containing one enzymatically active and inactive copy of the TIR domain .
N-terminal extension of GAT domain (GGA_N-GAT)
Type: Domain

This domain is found in the N-terminal region of the GGA and Tom1 (GAT) domain in Golgi-localizing gamma-adaptin ARF-binding protein 1 (GGA1). This domain can also be found in GGA2 and GGA3. The GAT domains is the key region in GGA that interacts with ARF. ARF plays a crucial role in docking adaptor proteins to membranes. This domain is referred to as N-GAT and it interacts extensively with ARF .

The GAT domain is a region of homology of ~130 residues, which is found in eukaryotic GGAs (for Golgi-localized, gamma ear-containing ADP ribosylation factor (ARF)-binding proteins) and vertebrate TOMs (for target of myb). The GAT domain is found in its entirety only in GGAs, although, at the C terminus it shares partial sequence similarity with a short region of TOMs. The GAT domain is found in association with other domains, such as VHS and GAE. The GAT domain of GGAs serves as a molecular anchor of GGA to trans-Golgi network (TGN) membranes via its interaction with the GTP-bound form of a member of the ARF family of small GTPases and can bind specifically to the Rab GTPase effector rabaptin5 and to ubiquitin .

The GGA-GAT domain possesses an all α-helical structure, composed of four helices arranged in a somewhat unusual topology, which has been called the helical paper clip. The overall structure shows that the GAT domain has an elongated shape, in which the longest helix participates in two small independent subdomains: an N-terminal helix-loop-helix hook and a C-terminal three-helix bundle. The hook subdomain has been shown to be both necessary and sufficient for ARF-GTP binding and Golgi targeting of GGAs. The N-terminal hook subdomain contains a hydrophobic patch, which is found to interact directly with ARF . It has been proposed that this interaction might stabilise the hook subdomain . The C-terminal three-helix bundle is involved in the binding with Rabaptin5 and ubiquitin .
CarS, SH3 domain (CarS_SH3)
Type: Domain

This is an SH3 domain found in antirepressor proteins such as CarS from Myxococcus xanthus. CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarS physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB operon. Structural studies of CarS from M. Xanthus reveals a β-barrel fold akin to that in SH3 domains. However, it diverges from the typical SH3 domain fold in the lengths and conformations of the connecting loops. Functional analysis reveal that SH3 domain-like fold in the antirepressor CasS, mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription .
FKBP3, basic tilted helix bundle domain (FKBP3_BTHB)
Type: Domain

This domain is found on the N-terminal region of peptidyl-prolyl cis-trans isomerase FKBP3 and in the core region of E3 ubiquitin ligase HectD1. It adopts a compact 5-helix bundle, hence termed BTHB (Basic Tilted Helix Bundle) domain. In FKBP3, it has been suggested to have a role in regulating the association state of nucleosomes by interacting with nucleolin. Moreover, this basic domain in FKBP35 forms alternative complexes with other chromatin-related proteins, such as the HDAC1, HDAC2, and the transcriptional regulator YY1, the DNA binding activity of which is enhanced on binding FKBP3. Structural analysis of this fold suggests that the DNA binding properties of FKBP3 and HectD1 are presented by the conserved basic region .
PTPRJ, transmembrane domain (PTPRJ_TM)
Type: Domain

Receptor-type protein tyrosine phosphatase that plays roles in cell adhesion, migration, proliferation and differentiation. PTP receptor type J (PTPRJ) possesses an extracellular region containing five fibronectin type III repeats, the transmembrane region included in this entry, and an intracytoplasmic catalytic domain . This entry probably contains part of a Fn3 domain at the N terminus.
Bacterial archaeo-eukaryotic release factor family 10 (BaeRF_family10)
Type: Family

This entry represents a bacterial family of the archaeo-eukaryotic release factor superfamily. It is likely to play roles in biological conflicts or regulation under stress conditions at the ribosome .
Bacterial Alpha-2-macroglobulin, MG5 domain (Bact_A2M_MG5)
Type: Domain

Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. This domain is found on the N-terminal region in A2Ms in bacteria. Structure analysis of Salmonella enterica ser A2Ms (SA-A2Ms) show that they are composed of 13 domains, all of which fold as variants of β sandwiches with the exception of the TED, which consists of 14 α helices. Most of the β sandwich domains appear to serve a structural role and are referred to as the macroglobulin-like (MG) domains. This is the MG5 domain .
RIG-I-like receptor, C-terminal (RIG-I-like_C)
Type: Domain

This entry represents the C-terminal domain of RIG-I and RIG-I-like receptors, which are key cytosolic pattern-recognition receptors of the vertebrate innate immune system that forms the first line of defence against RNA viral infection . ATP-dependent RNA helicase DHX58 (also known as RIG-I-like receptor LGP2) acts as a regulator of RIG-I and IFIH1/MDA5 mediated antiviral signaling as it cannot initiate antiviral signalling due to the lack of the CARD domain required for activating MAVS/IPS1-dependent signalling events. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'-triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA .
Copper resistance protein ScsC, N-terminal (ScsC_N)
Type: Domain

This is the N-terminal domain found in copper resistance protein ScsS present in Proteus mirabilis. ScsC is a powerful disulfide isomerase that is able to refold and reactivate the scrambled disulfide form of the model substrate RNase A. The protein has a thioredoxin 4 domain but, unlike other characterised proteins in this family, it is trimeric. The N-terminal domain is responsible for trimerization of ScsC which is needed for isomerase activity .
HEPN/RES N-terminal domain 1 (HEPN/RES_NTD1)
Type: Domain

This domain is mostly α helical. It is fused to HEPN (MAE_28990 superfamily), RES domain, a potential RNase found in various toxin systems .

The HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) domain is found in an enormous variety of defense and stress response systems .
NEDD8 ultimate buster 1, ubiquitin-like domain (NUB1_ubiquitin-like_dom)
Type: Domain

This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster 1.

NUB1 is an adaptor protein which negatively regulates the ubiquitin-like protein Nedd8 as well as neddylated proteins levels through proteasomal degradation . It has been shown to be regulated by Mdm2 (E3 ubiquitin ligase) through ubiquitination on its lysine 159 .
CD-NTase-associated protein 15 (Cap15)
Type: Domain

This entry includes CD-NTase-associated protein 15 (Cap15), an effector protein of a CBASS antivirus system that provides immunity against bacteriophages . Structure determination of Cap15 revealed that it has a compact 8-stranded β-barrel scaffold that forms a cyclic dinucleotide receptor domain that oligomerizes upon activation. Activated Cap15 binds the cyclic nucleotide second messenger 3',3'-cGAMP, relocalizes throughout the cell and specifically induces rupture of the inner membrane . These proteins have two transmembrane segments (TM) at the N-terminal, which is essential for phage protection .
Vesicle tethering protein p115, armadillo tether-repeat (P115_Arm_rpt)
Type: Repeat

This entry represents the armadillo-like tether-repeat of vesicle tethering protein p115 . This entry contains a single copy of the repeat unit.
NLRC5, atypical caspase recruitment domain (NLRC5_atypical_Card)
Type: Domain

This entry represents the N-terminal effector domain found in NLRC5. It adopts a six α-helix bundle with a general death fold. It possesses a fold similar to the one of the death-fold domains; however, it displays significant differences in the number of core α-helices and their relative orientation. Hence, it is suggested that NLRC5 belongs to the caspase recruitment domain (CARD) subfamily as an atypical CARD .
RNA ligase 1 (RLIG1)
Type: Family

This entry represents RNA ligase 1 from animals (RLIG1), which functions as an RNA ligase in vitro . This protein catalyses ATP-dependent RNA ligation via a three-step mechanism, involving tandem auto- and RNA AMPylation. It exhibits selectivity for single-stranded RNA substrates and may not have nick-sealing activity on double-stranded DNA-RNA hybrids . RLIG1 May play a role in maintaining RNA integrity under stress conditions, for example in response to reactive oxygen species (ROS) .
Vta1, C-terminal (Vta1_C)
Type: Domain

This is the C-terminal domain of the Vta1, which is a multivesicular body (MVB) protein. This domain promotes the ATP-dependent double ring assembly of Vps4. Furthermore, it has been shown that it is necessary and sufficient for protein dimerization. Mutations in Lys-299 and Lys-302 completely abolished the ability of Vta1 to stimulate the ATPase activity of Vps4 while mutation in Lys-322 had no effect .
Nitrosopumilus output domain 1 (NitrOD1)
Type: Domain

NitrOD1 (Nitrosopumilus output domain 1) is found in thaumarchaea, either in stand-alone form or in combination with the response regulator receiver domain (

) .
Dda helicase SH3 domain (SH3_14)
Type: Domain

This is a Src homology-3 (SH3) like β-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second β-ribbon that is referred to as the hook and a β-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA .
FlgO domain (FlgO_dom)
Type: Domain

This entry represents a domain found in the FlgO protein. Mutation of this protein in Vibrio cholerae has been shown to reduce motility. FlgO is an outer membrane protein that localises throughout the membrane and not at the flagellar pole. Although FlgO and FlgP do not specifically localize to the flagellum, they are required for flagellar stability. Proteins in this family mostly contain an N-terminal lipoprotein attachment motif .
Yeast SAGA-associated factor 11, N-terminal domain (Sgf11_N)
Type: Domain

The SAGA (Spt-Ada-Gcn5-Acetyltransferase) transcriptional co-activator is a protein complex that regulates inducible yeast genes by performing multiple functions including acetylating core histones, recruiting the RNA polymerase II preinitiation complex, and deubiquitinating histone H2B. The deubiquitinating activity of SAGA resides in a distinct sub-complex called the deubiquitinating module (DUBm), which consists of four proteins that are conserved across eukaryotes: Ubp8, Sgf11, Sus1 and Sgf73. The DUBm proteins are organized into two lobes around the globular domains of Ubp8 . In SAGA, Sus1 binds to Sgf11 by wrapping around this N-terminal domain of Sgf11, forming a stable dimer .
Cas9 C-terminal domain (Cas9_C)
Type: Domain

This is the C-terminal domain of Cas9 enzymes found mainly in actinobacteria .
Domain of unknown function DUF5606 (DUF5606)
Type: Domain

This domain is found at the N-terminal end of BVU_3817 from Phocaeicola vulgatus (

) and similar proteins mostly from Bacteroidetes. This domain adopts a β-barrel with SH3 topology and is usually found associated with

. Its function is unknown.
Phage tail lysozyme (Phage_lysozyme2)
Type: Domain

This domain has a lysozyme like fold. It is found in the tail protein of various phages probably giving them the ability to degrade the host cell wall peptidoglycan layer .
Large polyvalent protein associated domain 24 (LPD24)
Type: Domain

This is an all-beta domain that is mostly seen in polyvalent proteins of conjugative elements .
Anaphase-promoting complex subunit 1, C-terminal (APC1_C)
Type: Domain

This is the C-terminal domain of anaphase-promoting complex subunit 1 (APC1).

Apc1 is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes . Infection of human fibroblasts with human cytomegalovirus (HCMV) leads to cell cycle dysregulation, which is associated with the inactivation of the anaphase-promoting complex .
Primosomal protein N', 3' DNA-binding domain (PriA_3primeBD)
Type: Domain

This domain represents the N-terminal DNA-binding domain found in the PriA protein. This domain has been shown to bind the 3' end of the leading-strand arm of replication fork structures .

Primosomal protein N', also known as ATP-dependent helicase PriA, is a component of the primosome, which is involved in replication, repair, and recombination. PriA serves as a sensor/stabiliser for an arrested replication fork, which is lethal in bacteria if left unrepaired and eventually promotes restart of DNA replication through the assembly of a primosome. It also serves as a checkpoint protein that prevents the replicase from advancing in a strand displacement reaction on forks that do not contain a functional replicative helicase . This protein shows a modular arrangement in which its central helicase core is surrounded by several DNA-binding elements, including a 3'DNA-binding domain

at the N-terminal. This domain is usually followed by a circularly permuted winged helix (WH) domain

. At the C-terminal, there is a Cys-rich region (CRR) domain

, which is embedded within the C-terminal helicase lobe

, followed by the C-terminal domain (CTD)

.
ApeA, N-terminal domain (ApeA_NTD)
Type: Domain

This domain contains mostly β-strands. It is fused to HEPN (Apea). There are several conserved aromatic residues, abundant but poorly conserved .
Beta-porphyranase A, C-terminal (BPA_C)
Type: Domain

This domain is found towards the C-terminal end of beta-porphyranase A (BPA) from Bacteroides plebeius, a beta-galactanase that cleaves the beta-1,4 glycosidic bond and can also use methylated galactoses . This domain adopts a β sandwich shape . Beta-porphyranases, which are active on sulfated polysaccharides from marine red algae of the genus Porphyra, are present in marine bacteria .

This domain is also found in Beta-agarase AgaO from Microbulbifer thermotolerans, an endo-type beta-agarase and Funoran endo-beta-hydrolase from Wenyingzhuangia aestuarii, an endohydrolase that cleaves the beta-1,4 glycosidic bond between beta-D-galactopyranose-6-sulfate and 3,6-anhydro-alpha-L-galactopyranose unit of funoran .
Cas9, topo homolgy domain (Cas9_Topo)
Type: Domain

This is the Topo-homology domain found in Cas9 proteins from Actinobacteria. This domain bears structural similarity to a domain found in topoisomerase II .
Nitrososphaera output domain 2 (NitrOD2)
Type: Domain

NitrOD2 (Nitrososphaera output domain 2) is found in thaumarchaea, either in stand-alone form or in combination with the response regulator, receiver domain
.
Mu-like prophage FluMu N-terminal domain (FluMu_N)
Type: Domain

Structural analysis of HI1506 (also known as Mu-like prophage FluMu protein gp35) from Haemophilus influenzae showed that HI1506 consists of two structured domains connected by an unstructured 30 amino acid loop. This entry is the N-terminal domain which comprises a three-stranded antiparallel β-sheet packed against an α-helix .
Dynein heavy chain, C-terminal domain (Dynein_C)
Type: Domain

This family represents the C-terminal domain of dynein heavy chain. This domain is a complex structure comprising six α-helices and an incomplete six-stranded antiparallel β-barrel. The shape of this domain is distinctively flat, spreading over the AAA1, AAA5 and AAA6 domain .
Apea-like HEPN (HEPN_Apea)
Type: Domain

This is an Apea-like HEPN nuclease domain. In epsilonproteobacteria it is embedded in R-M operons .
FbpC, C-terminal regulatory nucleotide binding domain (FbpC_C)
Type: Domain

Most functional ABC transporters are composed of at least four sub-units: two trans-membrane (TM) domains where the transport process takes place and two cytoplasmic nucleotide binding domains (NBDs) providing the energy required for active transport . This entry is one of the two NBDs found at the the C-terminal domain of FbpC, ferric iron uptake transporter, from Neisseria gonorrhoeae. The C-terminal regulatory domain adopts two OB-folds per monomer. These are similar in topology to those seen in the NBD (nucleotide binding domain) from the maltose uptake ABC transporter, MalK. However, FbpC does not open as far as MalK when ATP is removed from their respective closed structures. This difference was suggested to be due to the substantial domain swap in the regulatory domain of FbpC .
FlgA, N-terminal (FlgA_N)
Type: Domain

This entry represents a presumed domain found N-terminal to the SAF-like domain in FlgA proteins.

FlgA is essential for flagellar biosynthesis and motility, and plays a significant role in biofilm formation in Campylobacter . It functions as a flagellar chaperone in P-ring assembly .
Nucleoplasmin-like domain (NPL)
Type: Domain

The nucleoplasmin-like NPL domain is present in Drosophila FKBP39 and a large number of chromatin-related proteins .
Alpha galactosidase, C-terminal domain (Melibiase_C)
Type: Domain

This domain is found at the C-terminal of alpha galactosidase enzymes, also known as Melibiases. It is also found in isomalto-dextranase (IMD) from Arthrobacter globiformis .
RavJ-like, C-terminal domain (RavJ-like_C)
Type: Domain

This domain is found at the C-terminal of proteins mainly from Legionella, including RavJ (lpg0944) from Legionella pneumophila (

), which is thought to be an effector of the Icm/Dot translocation system from this bacteria. This domain folds into an all-α structure . This domain was previously known as DUF5617.
Exportin-1, repeat 2 (Exp1_repeat_2)
Type: Repeat

Exportin 1 (Exp1) 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-, C-terminal and central repeats show slightly different structural arrangements, with N- and C- terminal repeats interacting with each other.
Primosomal protein N, C-terminal domain (PriA_C)
Type: Domain

This is the C-terminal domain found in PriA DNA helicase. The C-terminal domain (CTD) bears similarity to the S10 subunit which binds branched rRNA within the bacterial ribosome. The C-terminal domain is part of the helicase domain of PriA proteins. It acts together with the 3' DNA-binding domain to form a site for binding ssDNA-binding protein (SSB) .

Primosomal protein N', also known as ATP-dependent helicase PriA, is a component of the primosome, which is involved in replication, repair, and recombination. PriA serves as a sensor/stabiliser for an arrested replication fork, which is lethal in bacteria if left unrepaired and eventually promotes restart of DNA replication through the assembly of a primosome. It also serves as a checkpoint protein that prevents the replicase from advancing in a strand displacement reaction on forks that do not contain a functional replicative helicase . This protein shows a modular arrangement in which its central helicase core is surrounded by several DNA-binding elements, including a 3'DNA-binding domain

at the N-terminal. This domain is usually followed by a circularly permuted winged helix (WH) domain

. At the C-terminal, there is a Cys-rich region (CRR) domain

, which is embedded within the C-terminal helicase lobe

, followed by the C-terminal domain (CTD)

.
Adhesin BspA, variable domain (BspA_v)
Type: Domain

This domain is found in BspA protein present in Streptococcus agalactiae. BspA is an antigen I/II family polypeptide that confers adhesion linked to pathogenesis in group B Streptococcus. This domain is referred to as the variable domain (BspA-V). BspA-V is responsible for binding to scavenger receptor gp340. BspA-V adopts a fold that is distinct from those of other AgI/II family polypeptide variable domains .
Rap1a immunity protein (Rap1a)
Type: Domain

The structures of the immunity protein Rap1a , responsible for the inhibition and neutralization of Ssp1 endopeptidase, revealed two distinct folds. The structure of the Ssp1-Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. The Rap1a subunit displays a compact globular structure constructed from five α-helices that assemble to form the highly stable symmetric dimer .
Domain of unknown function DUF5605 (DUF5605)
Type: Domain

This domain is found in the C-terminal region of proteins carrying

and

. The C-terminal domain is carried by species such as Bacteroides vulgatus.