SII-SWORD/CoKE huggingface dataset:
Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding (M/V/L/I-tRNA-synth_anticd-bd)
Type: Domain

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

This domain is found methionyl, valyl, leucyl and isoleucyl tRNA synthetases. It binds to the anticodon of the tRNA.
Pseudin antimicrobial peptide (Antimicrobial_19)
Type: Family

Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa. The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides .
Aurein antibiotic peptide family (Aurein_antimicrobial_peptide)
Type: Family

This family of antibacterial peptides are secreted from the granular dorsal glands of Litoria aurea (Green and golden bell frog), Litoria raniformis (Southern bell frog), Litoria citropa (Australian blue mountains tree frog) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6 ; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides .
APOBEC-like, N-terminal (APOBEC_N)
Type: Domain

This domain is found at the N terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine.
Chromosomal replication initiator, DnaA C-terminal (DnaA_C)
Type: Domain

This entry represents the C-terminal domain of bacterial DnaA proteins that 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).

DnaA is a protein of about 50kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) .
Benzylsuccinate synthase gamma subunit (BssC)
Type: Family

BssC short protein (57 amino acids) has been described as the gamma-subunit of benzylsuccinate synthase from Thauera aromatica strain K172 . It catalyzes the addition of fumarate to the methyl group of toluene, leading to the formation of benzylsuccinate. TutF has been identified and described as highly similar to BssC in T. aromatica strain T1 .
CD80-like, immunoglobulin C2-set (CD80_C2-set)
Type: Domain

This entry represents the C2-set type domains found in the T-cell antigen CD80, as well as in related proteins. CD80 (B7-1) is a glycoprotein expressed on antigen-presenting cells . The shared ligands on CD80 and CD86 (B7-2) deliver the co-stimulatory signal through CD28 and CTLA-4 on T-cells, where CD28 augments the T-cell response and CTLA-4 attenuates it .

The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable;

), C1-set (constant-1;

), C2-set (constant-2;

) and I-set (intermediate;

) . Structural studies have shown that these domains share a common core Greek-key β-sandwich structure, with the types differing in the number of strands in the β-sheets as well as in their sequence patterns .

Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system .
Cadherin, N-terminal (Cadherin_N)
Type: Domain

Cadherins are a family of adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in all solid tissues of the organism which modulate a wide variety of processes including cell polarisation and migration . Cadherin-mediated cell-cell junctions are formed as a result of interaction between extracellular domains of identical cadherins, which are located on the membranes of the neighbouring cells. The stability of these adhesive junctions is ensured by binding of the intracellular cadherin domain with the actin cytoskeleton. There are a number of different isoforms distributed in a tissue-specific manner in a wide variety of organisms. Cells containing different cadherins tend to segregate in vitro, while those that contain the same cadherins tend to preferentially aggregate together. This observation is linked to the finding that cadherin expression causes morphological changes involving the positional segregation of cells into layers, suggesting they may play an important role in the sorting of different cell types during morphogenesis, histogenesis and regeneration. They may also be involved in the regulation of tight and gap junctions, and in the control of intercellular spacing. Cadherins are evolutionary related to the desmogleins which are component of intercellular desmosome junctions involved in the interaction of plaque proteins.

Structurally, cadherins comprise a number of domains: classically, these include a signal sequence; a propeptide of around 130 residues; a single transmembrane domain and five tandemly repeated extracellular cadherin domains, 4 of which are cadherin repeats, and the fifth contains 4 conserved cysteines and a N-terminal cytoplasmic domain . However, proteins are designated as members of the broadly defined cadherin family if they have one or more cadherin repeats. A cadherin repeat is an independently folding sequence of approximately 110 amino acids that contains motifs with the conserved sequences DRE, DXNDNAPXF, and DXD. Crystal structures have revealed that multiple cadherin domains form Ca2+-dependent rod-like structures with a conserved Ca2+-binding pocket at the domain-domain interface. Cadherins depend on calcium for their function: calcium ions bind to specific residues in each cadherin repeat to ensure its proper folding, to confer rigidity upon the extracellular domain and is essential for cadherin adhesive function and for protection against protease digestion.

This entry represents a cadherin domain that is usually found at the N terminus of cadherin proteins.
Citrate lyase ligase, C-terminal (Citrate_lyase_ligase_C)
Type: Domain

[Citrate (pro-3S)-lyase] ligase (

), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation .

The proteins in this entry represent the C-terminal domain of citrate lyase ligase.
COG4 transport protein, middle alpha-helical bundle (COG4_M)
Type: Domain

COG4 is a component of the conserved oligomeric Golgi (COG) complex which mediates the proper glycosylation of proteins trafficking through the Golgi apparatus. It is included in the CATCHR (complexes associated with tethering containing helical rods) family, which includes components of the exocyst, GARP, and DSL1 complexes and share structural and functional features: the α-helical bundles at the middle/C-terminal (described as domains A-D/E) and a N-terminal coiled-coil region . This domain is found in the middle region of COG4 and corresponds to domains B and C. Mutations in COG4 cause fatal congenital disorders of glycosylation (CDGs) in humans .
Cpl-7 lysozyme, C-terminal (Cpl_7_lyso_C)
Type: Domain

This domain was originally found in the C-terminal moiety of the Cp-7 lysin (lysozyme,

) encoded by Bacteriophage Cp-7 . It is also found in the cell wall hydrolases of human and life-stock pathogens. CW_7 repeats make up a cell wall binding motif .
mRNA splicing factor Cwf18-like (mRNA_splic_Cwf18-like)
Type: Family

The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) . This entry also includes Ccdc12 from animals and RXLR100 from Plasmopara viticola .
mRNA splicing factor Cwf21 domain (mRNA_splic_Cwf21_dom)
Type: Domain

The cwf21 domain is found in proteins involved in mRNA splicing. Proteins containing this domain have been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) . In yeast, this domain binds the protein Prp8p , a large and highly conserved U5 snRNP protein which has been proposed as a protein cofactor at the spliceosomal catalytic centre .

The cwf21 domain is found in, amongst others, the small Cwc21p protein in yeast as well as in the much larger human ortholog SRm300 (serine/arginine repetitive matrix protein).
Cytidine/deoxycytidylate deaminase, zinc-binding domain (Cyd/dCyd_deaminase_Zn-bd)
Type: Domain

This region contains the zinc-binding domain of cytidine and deoxycytidylate deaminase.
Bomanin (Bomanin)
Type: Family

Drosophila immune-induced molecules (DIMs), also know as bomanins, are short proteins induced during the immune response of Drosophila . The Bomanins (Boms) are a family of a dozen secreted peptides, this entry includes Bomanin Short 1-3/5/6, Bomanin Bicipital 1, and Bomanin Tailed2 which play a role in resistance to bacterial and fungal infections .
DNA primase DnaG, DnaB-binding domain (DNA_primase_DnaG_DnaB-bd_dom)
Type: Domain

Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB . This domain has a multi-helical structure that forms an orthogonal bundle .
Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
Type: Family

This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex .
INO80 complex, subunit Ies4 (INO80_su_Ies4)
Type: Family

The INO80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodelling complex. This family of proteins corresponds to the fungal Ies4 subunit of INO80.
Vacuolar fusion protein Ccz1 (Ccz1)
Type: Family

This entry includes the fungal vacuolar fusion protein Ccz1 which forms a complex with Mon1. The CCZ1-MON1 complex acts where vesicles fuse with the vacuole and is required in several vacuolar delivery pathways including autophagy, pexophagy and endocytosis as well cytoplasm to vacuole transport . Ccz1 interacts with a GTPase during fusion .
Ribosomal protein mS38, C-terminal (Ribosomal_mS38_C)
Type: Domain

This domain is found at the C-terminal end of mitochondrial small ribosomal subunit protein mS38 (also known as AURKAIP1 or COX24 in human and yeast, respectively). In yeasts is involved in the splicing of the COX1 mRNA . mS38 is a component of the mitochondrial ribosome (mitoribosome), responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane . This entry also includes uncharacterised proteins from bacteria.
Histone acetyltransferase Rtt109/CBP (Histone_AcTrfase_Rtt109/CBP)
Type: Family

Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal RTT109 protein, which is required for H3K56 acetylation . In Schizosaccharomyces pombe (Fission yeast) loss of RTT109 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin . RTT109 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast . This family also includes p300/CBP acetyltransferase, which has different catalytic properties and cofactor regulation to RTT109 . CREB-binding protein (CBP) is a transcriptional co-activator that acetylates both histones and non-histone proteins . CBP binds specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes .
Beta-catenin-like protein 1, N-terminal (CTNNBL1_N)
Type: Domain

This entry represents the N-terminal domain of the beta-catenin-like protein 1 (CTNNBL1). CTNNBL1 is a component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. In humans, it participates in AID/AICDA-mediated Ig class switching recombination (CSR) and may induce apoptosis .
Protein of unknown function DUF1719 (DUF1719)
Type: Family

This is a group of proteins of unknown function from Gramineae (grasses).
Domain of unknown function DUF1720 (DUF1720)
Type: Domain

This domain is found in different combinations with cortical patch components EF hand, SH3 and ENTH and is therefore likely to be involved in cytoskeletal processes. It is found in proteins of the actin cytoskeleton-regulatory complex.
DASH complex subunit Hsk3-like (Hsk3-like)
Type: Family

Hsk3 is a subunit of the DASH complex, a microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro .
Lactococcus phage c2, E2 (Lactococcus_phage_c2_E2)
Type: Family

This is a family of short conserved proteins of 37 amino acids, described in Lactococcus phage c2 and in related phage. The function of these proteins is unknown.
Translation elongation factor, KOW-like (Transl_elong_KOW-like)
Type: Domain

This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors.
Early nodulin 40 (ENOD40)
Type: Family

This entry represents the family of nodulin 40 proteins. The soybean early nodulin 40 (ENOD40) mRNA contains two short overlapping ORFs; in vitro translation yields two peptides of 12 and 24 amino acids . The putative role of the ENOD40 genes has been in favour of organogenesis, such as induction of the cortical cell divisions that lead to initiation of nodule primordia, in developing lateral roots and embryonic tissues. This supports the hypothesis for a role of ENOD40 in lateral organ development .
F-box associated domain, type 3 (F-box-assoc_dom_typ3)
Type: Domain

This domain occurs in a diverse superfamily of genes in plants. Most examples are found C-terminal to an F-box (

), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes . Some members have two copies of this domain.
Influenza matrix M1, C-terminal (Flu_matrix_M1_C)
Type: Domain

Matrix protein (M1) of Influenza virus is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of RNA-nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously. M1 is comprised of two domains connected by a linker sequence. The C-terminal domain contains α-helical structure and appears to be involved in growth and virulence of the virus .
Glycosyl hydrolase family 32, C-terminal (Glyco_hydro_32_C)
Type: Domain

This domain corresponds to the C-terminal domain of glycosyl hydrolase family 32. It forms a β sandwich module .
Glycosyl hydrolase family 98, C-terminal (GH98_C)
Type: Domain

This domain can be found in the C terminus of the blood-group-substance endo-1,4-beta-galactosidase EabC from Clostridium perfringens, which is a member of the glycosyl hydrolase family 98. EabC is an endo-beta-galactosidase capable of releasing both the blood group A trisaccharide (A-Tri; GalNAcalpha1-->3(Fucalpha1-->2)Gal) and B trisaccharide (B-Tri; Galalpha1-->3(Fucalpha1-->2)Gal) glycotopes from blood group A- and B-containing glycoconjugates, respectively . This domain is not expected to form part of the catalytic activity.
Glycosyl hydrolase family 98, central domain (GH98_central)
Type: Domain

This domain can be found in the central of the blood-group-substance endo-1,4-beta-galactosidase EabC from Clostridium perfringens, which is a member of the glycosyl hydrolase family 98. EabC is an endo-beta-galactosidase capable of releasing both the blood group A trisaccharide (A-Tri; GalNAcalpha1-->3(Fucalpha1-->2)Gal) and B trisaccharide (B-Tri; Galalpha1-->3(Fucalpha1-->2)Gal) glycotopes from blood group A- and B-containing glycoconjugates, respectively .
Hepatitis C virus, Non-structural 5a protein, domain 1a (HCV_NS5A_1a)
Type: Domain

The exact function of the Hepatitis C non-structural 5A (NS5A) protein is not known, but it is an active component of the replicase, regulates replication and modulates a range of cellular processes including innate immunity and dysregulated cell growth. NS5A is organised into three domains, labelled I, II and III. Domain I contains a zinc-binding motif and an amphipathic N-terminal helix which promotes membrane association. Mutations disrupting either the membrane anchor or zinc binding are lethal for RNA replication .

This entry represents the 1a domain of NS5A. It binds zinc, which is thought to be crucial for fold maintenance and is essential for replicase function .
Hepatitis C virus non-structural 5a, 1B domain (HCV_NS5a_1B_dom)
Type: Domain

The exact function of the Hepatitis C non-structural 5A (NS5A) protein is not known, but it is an active component of the replicase, regulates replication and modulates a range of cellular processes including innate immunity and dysregulated cell growth. NS5A is organised into three domains, labelled I, II and III. Domain I contains a zinc-binding motif and an amphipathic N-terminal helix which promotes membrane association. Mutations disrupting either the membrane anchor or zinc binding are lethal for RNA replication .

This entry represents the 1b domain of NS5A. It consists of two distinct anti-parallel β-sheets surrounded by extensive random coil structures . This domain contains a disulphide bond near its C-terminal not required for the RNA replicase functions of NS5A. The presence of the cited sulphide bond suggests that it is likely responsible of the structural arrangement of domains II and III, thus playing a regulatory role in NS5A function by serving as a conformation switch to modulate functions of NS5A in and out of the replicase .
Histone deacetylase interacting domain (HDAC_interact_dom)
Type: Domain

This domain is found in the transcriptional repressor Sin3. It forms interactions with histone deacetylases .

Budding yeast Sin3 is a component of both the Rpd3S and Rpd3L histone deacetylase complexes . In mammals there are two Sin3 paraologues, Sin3A and Sin3B. They forms the larger Sin3L/Rpd3L and the smaller Sin3S/Rpd3S complexes, both complexes rely largely on HDAC (histone deacetylase) activity to affect transcriptional repression. Sin3A and Sin3B may partition into the Sin3L/Rpd3L and Sin3S/Rpd3S complexes, respectively .
Hepatitis B virus, capsid N-terminal (Hepatitis_B_virus_capsid_N)
Type: Domain

This entry represent a short region found at the N terminus of some viral capsid (HBcAg) proteins from various Hepatitis B virus (HBV), which is a major human pathogen. The conservation of four Cys residues suggests that this region acts as a zinc binding domain.

Hepatitis virus is composed of an outer envelope of host-derived lipid containing the surface proteins, and an inner protein capsid that contains genomic DNA. The capsid is composed of a single polypeptide, HBcAg, also known as the core antigen. The capsid has a 5-helical fold, where two long helices form a hairpin that dimerises into a 4-helical bundle ; this fold is unusual for icosahedral viruses. The monomer fold is stabilised by a hydrophobic core that is highly conserved among human viral variants. The capsid is assembled from dimers via interactions involving a highly conserved arginine-rich region near the C terminus. This viral capsid acts as a core antigen, the major immunodominant region lying at the tips of the α-helical hairpins that form spikes on the capsid surface.
Helix-turn-helix, type 11 (HTH_11)
Type: Domain

Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small β-sheets. The winged helix motif consists of two wings (W1, W2), three α helices (H1, H2, H3) and three β-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 . The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions.

This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon . It is also found in other proteins including regulators of amino acid biosynthsis such as LysM , and regulators of carbohydrate metabolisms such as LicR and FrvR .