SII-SWORD/CoKE huggingface dataset:
AbiJ, N-terminal domain 5 (AbiJ_NTD5)
Type: Domain

This domain is mostly α helical. It is found fused to AbiJ-like HEPN, and to other domains presumably involved in defense .
CdiI, C-terminal (CdiI_C)
Type: Domain

This is the C-terminal domain of Contact-dependent growth inhibition immunity (CdiI) proteins present in Enterobacter cloacae. CdiI proteins neutralize CdiA-CT toxins to protect toxin-producing cells from auto-inhibition. Structural homology searches reveal that Enterobacter cloacae's CdiI is most similar to the Whirly family of single-stranded DNA-binding protein .
Astrotactin-2, C-terminal beta-hairpin domain (ASTN_2_hairpin)
Type: Domain

This is a β-hairpin domain found at the C-terminal region of astrotactin 2 proteins (ASTN-2). ASTN-2 is an integral membrane perforin-like protein linked to the planar cell polarity pathway in hair cells. It consists of multiple polypeptide folds: a perforin-like domain, a minimal epidermal growth factor-like module, a fibronectin type III domain Fn (III) and an annexin-like domain as well as the β hairpin domain which packs across the fibronectin domain .
Adenylyl/Guanylyl and SMODS, C-terminal sensor domain (AGS_C)
Type: Domain

This entry represents a sensor domain found in cytidylate cyclase (PycC, clade E) and cyclic GMP-AMP synthase (CdnB) from E.coli , which are involved in immunity against bacteriophage . PycC and CdnB are part of the Pycsar (pyrimidine cyclase system for antiphage resistance) and CBASS system respectively, which are closely related; both of these proteins synthesize cyclic nucleotides in response to infection which serve as specific second messenger signals that activate the adjacent effectors. This domain (AGS-C) adopts a Ig-like fold and it has been suggested to mediate phage detection .
Large polyvalent-protein-associated domain 15 (LPD15)
Type: Domain

This is a predicted enzymatic alpha and beta domain . It is found at the N terminus of polyvalent proteins of conjugative elements .
Mutator 2, fork head associated domain (MU2_FHA)
Type: Domain

This is the N-terminal forkhead-associated (FHA) domain found in Drosophila mutator 2 (MU2) protein. FHA domains are generally phosphothreonine (pThr) specific-binding domains and are present in DNA repair and checkpoint proteins. However, phosphothreonine binding is not conserved in the MU2 active site pocket due to the absence of three key residues needed for pThr binding. Dimerization, is conserved between FHA domains of Drosophila MU2 and human MDC1 albeit through different interfaces. The MU2 FHA domain dimerizes via the β-sheet 2, the MDC1 FHA domain dimerizes via the opposite β-sheet 1 .
C4b-binding protein alpha, oligomerization domain (C4bp_oligo)
Type: Domain

This is the C-terminal oligomerization domain found in C4b-binding protein (C4BP), which contains 14 cysteines that form 7 intermolecular disulfide bridges. C4BP is a plasma glycoprotein complex of 570kDa, which is mainly produced in the liver. C4BP is the major inhibitor of complement activation, the major isoform consists of 7alpha and one beta-chain where each alpha-chain comprises eight complement control domain proteins (CCPs) and a C-terminal oligomerization domain. This domain carries a stretch of 42-45 amino acids that has been shown to be required for ring formation .
Phosphoethanolamine N-methyltransferase 2, N-terminal (PMT2_N)
Type: Domain

This is the N-terminal vestigial domain found in Haemonchus contortus phosphoethanolamine N-methyltransferases 2 (PMT2). Structural analysis reveal changes leading to loss of function in the vestigial domains of the nematode PMT .
Nucleotidyltransferase, substrate binding domain (Ant(4')-IIb_substrate-bd)
Type: Domain

This domain is located on the central part of a nucleotidyltransferase from Pseudomonas aeruginosa (Ant(4')-IIb) and in other bacterial proteins predominantly found in Actinobacteria. It shows a four-helical up-and-down bundle and is found associated with other nucleotidyltransferase domains.
Chalcone isomerase, N-terminal (Chalcone_N)
Type: Domain

This is the N-terminal domain of chalcone isomerase present in Eubacterium ramulus. Chalcone isomerase is involved in the degradation pathway of flavone naringenin .
LepB, N-terminal (LepB_N)
Type: Domain

Rab GTPases constitute the largest family of small GTP-binding proteins that act as molecular switches in regulating vesicular transport in eukaryotic cells. LepB is a Rab GTPase-activating protein (GAP) effector found in Legionella pneumophila. This entry represents the N-terminal domain which is followed by a GAP domain .
Importin 13 repeat (Importin_rep_3)
Type: Repeat

Importin 13 serves as receptor for nuclear localization signals (NLS) in cargo substrates . It mediates docking of the importin/substrate complex to the nuclear pore complex (NPC). It contains several repeats structurally similar to the HEAT repeat . This entry represents a single repeat unit.
Kyakuja-Dileera-Zisupton transposase (KDZ)
Type: Family

A transposase family with an RNaseH catalytic domain, often fused to DNA binding domains such as SAP or cysteine cluster domains. KDZ transposases are widely present in fungi, metazoa, chlorophytes and haotpohytes. Fungal versions are often associated with a TET/JBP family of dioxygenases .
Dipeptidyl peptidase 4, low complexity region (DPPIV_rep)
Type: Domain

Dipeptidyl peptidase IV includes a helical region, the N-terminal domain and the catalytic domain. This entry represents a sequence that can be repeated in the low complexity region between the helical N terminus and the N-terminal domain.
Siroheme decarboxylase , AsnC-like ligand binding domain (AsnC_trans_reg2)
Type: Domain

This entry contains an AsnC-like ligand binding domain. This domain can be found in siroheme decarboxylases .
E3 ubiquitin-protein ligase HECW1, helical box domain (HECW1_helix)
Type: Domain

This is a region of 109 amino acids found in HECW1 proteins in Eukaryotes. Polymorphisms in the same region in the C.elegans homologue affects C. elegans behavioural avoidance of a lawn of Pseudomonas aeruginosa .
UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 (UGGT_TRXL_4)
Type: Domain

This is the fourth TRXL (thioredoxin-like) domain found in UDP-glucose:glycoprotein glucosyltransferase (UGGT) .
Inulin fructotransferase, beta helix repeat (Beta_helix_2)
Type: Repeat

This region contains a right-handed parallel β-helix repeat unit found in inulin fructotransferase . This entry includes sequences not found in

.
Porphyranase, beta-sandwich domain 1 (Beta-sand_Porphyrn)
Type: Domain

This domain is found in porphyranase protein present in Bacteroides plebeius. Porphyranase breaks down porphyran during digestion of red seaweed glycans. It is worth noting that red seaweed glycans contain sulfate esters that are absent in terrestrial plants. This domain follows the catalytic domain of the porphyranase protein and adopts a β-sandwich .

This domain is also found in Beta-agarase which is involved in cleavage of agar at the (1->4) linkage, producing tetrameric saccharide molecules . It follows the (β/α)8 barrel catalytic domain and folds into a β-sandwich .
Lectin-like domain (Lectin-like)
Type: Domain

This is a lectin like domain found in Cwp84, a surface-located cysteine protease (a member of the C1A cysteine protease family, also known as papain proteases) responsible for the maturation of the SlpA precursor protein which has been implicated in the degradation of extracellular matrix proteins such as fibronectin, laminin and vitronectin. Structural comparison indicates that this domain is similar to carbohydrate-binding domains .
Protein CROC-4 (CROC-4)
Type: Family

Members of this family are 18kDa serine/threonine-rich polypeptides containing a P-loop motif and an SH3-binding region with phosphorylation sites for a variety of protein kinases (cdc2, CDK2, MAPK, CDK5, protein kinase C, Ca2/calmodulin protein kinase 2, casein kinase 2) involved in cell proliferation and differentiation. Functional studies revealed that expression is associated with proliferating and migrating cells in developing brain. Furthermore, it has been suggested that CROC-4 participates in brain-specific c-fos signaling pathways involved in cellular remodeling of brain architecture . C1orf61 expression was also found associated with the progression of liver disease as well as human embryogenesis. It was shown to be up-regulated in hepatic cirrhosis tissues and further up-regulated in primary hepatocellular carcinoma tumors where it was suggested to play a role as a tumor activator .
Type VI secretion system TssR-like, N-terminal barrel domain (T6SS_TssR-like_N)
Type: Domain

This entry represents the N-terminal small β-barrel domain from TssR. TssR proteins have no predicted TM regions.

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Domain of unknown function DUF5623 (DUF5623)
Type: Domain

This is a domain of unknown function found mainly in proteobacteria.
MapZ, extracellular C-terminal domain 2 (MapZ_C2)
Type: Domain

In the pneumococcus cell division, MapZ (Midcell Anchored Protein Z) locates at the division site before FtsZ and guides septum positioning. MapZ forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ-ring through direct protein-protein interactions . Structural analysis indicate that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. The extracellular C-terminal domain carries a conserved patch of amino acids which plays a crucial function in binding peptidoglycan and positioning MapZ at the cell equator .
Elongation factor 3, four helical bundle domain (EF3_4HB)
Type: Domain

This entry represents a domain found in elongation factor 3A where it packs against the bottom of the concave face of the HEAT domain .
Calcium binding protein SSO6904 (Ca_bind_SSO6904)
Type: Domain

This domain is SSO6904 present in Sulfolobus solfataricus. SSO6904 is a calcium binding protein thought to have a weak affinity for other cations such as Mg2+ and Zn2+. The structure of SSO6904 is similar to that of saposin-fold proteins. Saposin proteins are membrane-interacting glycoproteins required for the hydrolysis of certain sphingolipids by specific lysosomal hydrolases .
NLRC4, helical domain (NLRC4_HD)
Type: Domain

This is a helical domain found in NLRC4, an nucleotide-binding and oligomerization domain-like receptor (NLR) protein. Structural and functional studies indicate that the helical domain HD2 repressively contacted a conserved and functionally important α-helix of the NBD (nucleotide binding domain) in NLRC4. Furthermore, the HD2 domain was shown to cap the N-terminal side of the LRR (leucine-rich repeat) domain via extensive interactions . Other proteins carrying this domain include baculoviral IAP repeat-containing protein 1 (Birc1), also known as neuronal apoptosis inhibitory protein (Naip).
ASP external chaperone (ASPCH)
Type: Domain

This domain is found in ASP external chaperone (ASPCH, also known as ORF 2), a protein encoded just downstream of asp (A. sobria serine protease) which is required for the production of the active form of the Aeromonas extracellular serine protease (ASP) and essential for its proper folding .
Domain of unknown function DUF5612 (DUF5612)
Type: Domain

This is a domain of unknown function which is mostly found C-terminal to the ACT domains.
Cch, helix turn helix domain (Cch_HTH)
Type: Domain

Staphylococcal Cassette Chromosome, or SCC elements, are a family of genomic islands found in S. aureus and closely related species. SCC elements that carry the mecA gene are called SCCmec and render S. aureus methicillin-resistant, creating the MRSA strains. Cch, the self-loading helicase encoded by SCCmec type IV, belongs to the pre-sensor II insert clade of AAA+ ATPases, as do the archaeal and eukaryotic MCM-family replicative helicases. The central domain (residues 157-438) contains an AAA+ ATPase fold. This domain is found at the C-terminal region, it is a winged helix-turn-helix (WH) domain typical of many dsDNA-binding proteins .
WRNIP1, ubiquitin-binding domain (Znf-WRNIP1_ubi)
Type: Domain

This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ .
Ribonuclease III, N-terminal domain (RNase_3_N)
Type: Domain

This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III). Structure analysis of Saccharomyces cerevisiae RNase III (known as Rnt1) revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity .
Metanogen output domain 2 (MetOD2)
Type: Domain

MetOD2 (Metanogen output domain 2) is found in euryarchaeal class Methanomicrobia, usually in combination with the receiver domain (

) .
HMW1 domain 2 (HMW1_D2)
Type: Domain

This domain is 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 and O-glycosylation of sugar acceptor sites. This domain forms an all alpha domain (AAD) when combined with the N-terminal domain. The AAD interacts extensively with the C-terminal GT-B fold in order to create a unique groove with the potential to accommodate the acceptor protein .
DICER-like, HTH domain (DICER_HTH)
Type: Domain

This entry represents the winged HTH domain found in the kinetoplastid DICER-like (DCL) enzymes, situated N-terminal to the KptA_kDCL domain

.
Rege-1, UBA-like domain (Rege-1_UBA-like)
Type: Domain

This entry represents a UBA-like domain found at the N terminus of ribonuclease ZC3 proteins, such as Rege-1 from C. elegans . Rege-1 is an endonuclease which binds to the 3'UTR of target mRNAs and induces degradation of the transcript . Proteins containing this domain also include ZC3H12A/B/C/D from humans.
Immunity protein CdiI (CdiI)
Type: Family

Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI+ bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighbouring target bacteria and produce CDI immunity proteins (CdiI) which bind CdiA-CT domains and neutralize their toxic activity to protect against self-inhibition. CdiI immunity proteins are also variable and only neutralize their cognate CdiA-CT toxins. Structure analysis of CdiI from Escherichia coli 536 (EC536) shows that is composed of a single domain and that it blocks the interaction with substrate, strongly suggesting that the immunity protein occludes the nuclease active site .
BepA, intracellular delivery domain (BepA_ID)
Type: Domain

This is a C-terminal domain found in BepA proteins from Bartonella henselae. It is a type IV secretion system (T4SS) effector protein. BepA from Bartonella henselae is composed of an N-terminal Fic domain and a C-terminal Bartonella intracellular delivery (ID) domain, the latter being responsible for T4SS-mediated translocation into host cells. The ID domain of BepA mediates inhibition of apoptosis and exhibits an OB (oligonucleotide/oligosaccharide binding)-fold .
Domain of unknown function DUF5613 (DUF5613)
Type: Domain

This is a domain of unknown function found in bacteria.
Prim-pol family 5 (PPL5)
Type: Domain

This entry represents the primase domain of prim-pol enzymes, currently known only in kinetoplastids .
DNMT3, cysteine rich ADD domain, GATA1-like zinc finger (DNMT3_ADD_GATA1-like)
Type: Domain

This entry represents the C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3 proteins.

The ADD domain is composed of three clearly distinguishable modules that pack
together through extensive hydrophobic interactions to form a single globular
domain. Packed against the N-terminal GATA1-like finger there is a second subdomain,
which binds two zinc ions and closely resembles the structure reported for
several PHD fingers. Finally, there is a long C-terminal α-helix that runs
out from the PHD finger and makes extensive hydrophobic contacts with the N-
terminal GATA1-like finger, bringing the N- and C-termini of the ADD domain close
together. This combination of fused GATA1-like and PHD fingers within a single
domain is thus far unique .

The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. Furthermore, the ADD domain of DNMMT3A (ADD-3A) competes with the chromodomain (CD) of heterochromatin protein 1 alpha (HP1alpha, CDHP1alpha) for binding to the H3 tail. The DNA methyltransferase (DNMT) 3 family members DNMT3A and DNMT3B and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development .
Toxoflavin-degrading enzyme (TxDE)
Type: Domain

This domain is found in toxoflavin-degrading enzymes such as toxoflavin lyase (TflA), also known as toxoflavin-degrading enzyme (TxDE). TflA/TxDE is structurally similar to the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity .
Peroxisomal membrane protein PEX14-like, KPWE domain (KPWE_PEX14_dom)
Type: Domain

This domain, previously known as DUF5572, is found in Peroxisomal membrane protein PEX14 from Arabidopsis thaliana and other eukaryotic proteins including human Peroxisomal biogenesis factor 39 (PEX39). PEX14 is a component of the PEX13-PEX14 docking complex, a translocon channel that specifically mediates the import of peroxisomal cargo proteins bound to PEX5 receptor. This domain carries a highly conserved KPWE sequence at the C-terminal.
Cas9, PI domain (Cas9_PI2)
Type: Domain

This domain is found in Cas9 proteins from some bacteria, such as Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. When this domain is combined with the C-terminal domain it is called the Pam-interacting (PI) domain. The Cas9 orthologs from different microbes have highly divergent sequences but their PI domains share a conserved core fold and recognize distinct PAM sequences .
Predicted pPIWI-associating nuclease (pP_pnuc_1)
Type: Domain

Predicted nuclease effector domain associating with prokaryotic PIWI-centred conflict systems .
VIP1, N-terminal (VIP1_N)
Type: Domain

This domain is found at the N terminus of inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1/2 (VIP1/2, or PPIP5K1/2) and related proteins. Structure analysis of human PPIP5K2 indicate that this region forms α-β-α domain . PPIP5K2 is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organismic homeostasis .
tRNA nuclease CdiA, C-terminal (CdiA_C)
Type: Domain

Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighbouring bacterial cells. CDI is mediated by the CdiB/CdiA family of two-partner secretion proteins. This domain represents the C-terminal of CdiA proteins (CdiA-CT), which contains the CDI toxin activity. The C-terminal nuclease domain forms a stable complex with its cognate immunity protein. It is also sufficient to inhibit growth when expressed in E. coli cells, consolidating the idea that they constitute the functional CDI toxin. The CdiA-CT C-terminal domains are structurally similar to type IIS restriction endonucleases suggesting that the toxins have metal-dependent DNase activity .
Synaptonemal complex protein 2, Spt16M-like domain (SYCP2_SLD)
Type: Domain

Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The SLD structure is highly similar to the middle domain of the histone chaperone FACT. It consists of a twisted ten-stranded β-sheet flanked by two helices. Since the SLD domain structurally resembles Spt16M, which is known as the well-recognized histone protein H2A-H2B; it is speculated that the SLD subdomain may be involved in chromatin binding .
Large polyvalent protein associated domain 38 (LPD38)
Type: Domain

This is an α and β fold domain found in polyvalent proteins of phages and prophages .
Prim-pol 4 (PPL4)
Type: Family

This entry represents a family of prim-pol enzymes with predicted roles in RNA processing and repair, potentially acting independently of a DNA template .
CxC3 like cysteine cluster (CxC3-like)
Type: Domain

This entry represents a predicted Zinc chelating domain present N-terminal to the KDZ transposase domain .
Benzylsuccinate synthase beta subunit (BssB_TutG)
Type: Domain

Proteins containing this domain include benzylsuccinate synthase beta subunit found in bacteria. BssB acts as a regulator of activation and may additionally be involved in regulating access to the enzyme's active site. It adopts a fold similar to that of a high potential iron-sulfur protein (HiPIP) and resembles the single small subunit of HPAD, which is known as the HpdC or HPADgamma in that system .
Interleukin-13 receptor subunit alpha-1, Ig-like domain (Il13Ra_Ig)
Type: Domain

This is the N-terminal Ig-like domain found in interleukin-13 receptor subunit alpha-1 (IL13RA1). IL13RA1 contains an extra N-terminal Ig-like domain not found in other receptors of the the common gamma-chain subfamily. The extra N-terminal Ig-like domain contacts the dorsal surfaces of both IL-4 and IL-13. The deletion of this domain has been shown to affect the binding of IL-13 to IL-13Ralpha1 .
RctB, helix turn helix domain (RctB_HTH)
Type: Domain

RctB is a highly conserved 75.3kDa protein (658 residues), which is unique to the Vibrionaceae. The first 500 amino acids of RctB are sufficient to mediate oriCII-based replication and its C-terminal 165 residues may mediate regulatory processes. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. This entry describes domain 1 located at the N-terminal region of RctB proteins. Mutational analysis shows that it binds oriCII DNA, and that this function is critical for the capacity of RctB to mediate oriCII-based replication .
Large polyvalent protein-associated domain 16 (LPD16)
Type: Domain

This is an α and β fold domain that is mainly found in polyvalent proteins of conjugative elements .
Reverse gyrase, zinc finger (Znf_Rg)
Type: Domain

This is the N-terminal zinc finger domain present in reverse gyrase proteins. Most reverse gyrases conserve the N-terminal zinc finger of the zinc ribbon type, pointing to a crucial function of this domain. Structure of Thermotoga maritima reverse gyrase elucidates that the N-terminal zinc finger firmly attaches the H1 (helicase 1) domain to the topoisomerase domain contributing to double-strand DNA (dsDNA) binding .