SII-SWORD/CoKE huggingface dataset:
Septum formation initiator FtsL/DivIC (FtsL/DivIC)
Type: Family

FtsL and DivIC (FtsB) are essential components of this division machinery . In Bacillus subtilis DivIC is necessary for both vegetative and sporulation septum formation . These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer .
Mycothiol-S-transferase (MST-like)
Type: Family

This entry, previously known as DUF664, represents the Mycothiol S-transferase (MST) from Mycobacterium tuberculosis and related proteins mainly found in Actinobacteria. MST binds to and is responsible for the transfer of Mycothiol (MSH) to xenobiotic acceptors. The ability of MST to catalyse this reaction depends on the presence of divalent metal ions and this enzyme exhibits only a residual activity in metal absence . MST is a member of the DinB-like superfamily (

). It folds into a canonical four-helical bundle that creates a metal binding site using a combination of three highly conserved coordinating histidine and aspartate residues. It was shown that MST uses Fe2+ as the catalytic metal in vivo .
Protein phosphatase inhibitor 2 (IPP-2) (PPI-2)
Type: Family

Protein phosphatase inhibitor 2 (IPP-2) is a phosphoprotein conserved among all eukaryotes, and it appears in both the nucleus and cytoplasm of tissue culture cells . Protein phosphatase inhibitor 2 family member C (PPP1R2C) has been shown to inhibit the catalytic subunit of PP1 .
Nmd3, N-terminal (Nmd3_N)
Type: Domain

Nmd3 acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit . This N-terminal region contains four conserved CXXC motifs that could be metal binding.
HPP (HPP)
Type: Family

This entry represents a family of integral membrane proteins from all cellular organisms, including At3g47980 from Arabidopsis thaliana (

), which is involved in nitrite transport . Members of this family have at least four transmembrane spanning helices. The most conserved region of an alignment of the proteins is a motif HPP. The specific role of these proteins is uncertain.
RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)
Type: Domain

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking .
Tail sheath protein (Tail_sheath)
Type: Family

This entry represents tail sheath proteins from various bacteriophages , including GpL from Bacteriophage Mu and Gp18 from Bacteriophage T4 .
Transposase, IS801/IS1294 (Transposase_32)
Type: Domain

Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This entry represents a domain found at the C-terminal of transposases IS1294 and IS801, found associated with a zinc finger domain at the N-terminal (

) .
GPI ethanolamine phosphate transferase 1 (GPI_EtnP_transferase_1)
Type: Family

This entry represents GPI ethanolamine phosphate transferase 1 enzymes, including the yeast enzyme MCD4 and the mammalian homolgoue PIG-N (also known as phosphatidylinositolglycan class N) . These enzymes are multi-pass endoplasmic reticulum membrane proteins involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. These enzymes transfer ethanolamine phosphate to the first alpha-1,4-linked mannose of the GPI precursor of the GPI-anchor. Ethanolamine phosphate on the alpha-1,4-linked mannose is essential for further mannosylation by GPI10 and is necessary for an efficient recognition of GPI lipids and GPI proteins by the GPI transamidase, for the efficient transport of GPI anchored proteins from endoplasmic reticulum to Golgi and for the physiological incorporation of ceramides into GPI anchors by lipid remodeling. MCD4 is also involved in non-mitochondrial ATP movements across the membrane and participates in Golgi and endoplasmic reticulum function, and is required for the incorporation of BGL2 into the cell wall.
A-kinase anchoring protein 95 (AKAP95) (AKAP95)
Type: Family

A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA .
Rhamnosyl O-methyltransferase (RNMT_CmcI)
Type: Family

This entry contains Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) . Members of this family are about 220 amino acids long. It also includes the CmcI protein

, which was previously thought to represent the cephalosporin-7--hydroxylase , however, it is apparently a methyltransferase that works with hydroxylase CmcJ, and its most likely function is to catalyse the transfer of a methyl group from SAM to the 7alpha-hydroxy cephalosporin in the second catalytic reaction of cephamycin formation. Studies using recombinant proteins purified from E. coli suggest that the complex, but not the separate proteins, exhibits a strong interaction with SAM and cephalosporin C .
RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)
Type: Domain

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (

) .
LicD/FKTN/FKRP, nucleotidyltransferase domain (LicD/FKTN/FKRP_NTP_transf)
Type: Domain

The LicD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent . These proteins are part of the nucleotidyltransferase superfamily .

Ribitol-5-phosphate transferase FKTN (also known as Fukutin), which is a member of the LicD family, is a mammal protein which may be involved in the modification of glycan moieties of alpha-dystroglycan; defects in Fukutin are associated with congential muscular dystrophy . Ribitol 5-phosphate transferase FKRP (also known as Fukutin-related protein), responsible for the the second step in the formation of the ribose 5-phosphate tandem repeat after FKTN activity , has N-terminal stem and C-terminal catalytic domains, and adopts a tetramer assembly .

This entry represents the nucleotidyltransferase domain.
RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)
Type: Domain

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module . This family appears to be specific to the largest subunit of RNA polymerase II.
TfoX, N-terminal (TfoX_N)
Type: Domain

This entry represents the N-terminal domain of TfoX from Haemophilus influenzae. TfoX Positively regulates genes required for DNA transformation (late competence-specific genes) in association with CRP .
TfoX, C-terminal (TfoX_C)
Type: Domain

This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes . This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with

in

.
Haem exporter protein D (CcmD) (Haem_export_protD_CcmD)
Type: Family

The CcmD protein is part of a C-type cytochrome biogenesis operon . CcmD interacts with CcmE and CcmC, establishing a cytoplasm to periplasm haem delivery pathway . CcmD is a component of the CcmABC ATP-binding cassette transporter complex. It is not necessary for the CcmC-dependent transfer of heme to CcmE in the periplasm but it is required for the release of holo-CcmE from the CcmABCD complex .
Succinylarginine dihydrolase (SuccinylArg_d-Hdrlase_AstB)
Type: Family

Succinylarginine dihydrolase (AstB) transforms N(2)-succinylglutamate into succinate and glutamate. This enzyme is the second in the five-step ammonia-producing arginine succinyltransferase pathway, the major pathway in Escherichia coli and in other related bacteria for arginine catabolism as a sole nitrogen source. AstB assumes a five-stranded α/β propeller structure, placing it in the amidinotransferase (AT) superfamily of proteins, which are characterised by their Cys-His-Glu active site triad .
RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)
Type: Domain

RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand .
RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)
Type: Domain

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound .
RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)
Type: Domain

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors .
BRICHOS domain (BRICHOS_dom)
Type: Domain

The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer, including BRI-2, chondromodulin-I (ChM-I), CA11, and surfactant protein C . Its exact function is unknown; roles that have been proposed for it include (a) targeting the protein to the secretory pathway, (b) an intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system .
DNA/pantothenate metabolism flavoprotein, C-terminal (DNA/pantothenate-metab_flavo_C)
Type: Domain

This entry represents the C-terminal domain found in DNA/pantothenate metabolism flavoproteins, which affects synthesis of DNA and pantothenate metabolism. These proteins contain ATP, phosphopantothenate, and cysteine binding sites. The structure of this domain has been determined in human phosphopantothenoylcysteine (PPC) synthetase and as the PPC synthase domain (CoaB) from the Escherichia coli coenzyme A bifunctional protein CoaBC . This domain adopts a 3-layer α/β/α fold with mixed β-sheets, which topologically resembles a combination of Rossmann-like and ribokinase-like folds. The structure of these proteins predicts a ping pong mechanism with initial formation of an acyladenylate intermediate, followed by release of pyrophosphate and attack by cysteine to form the final products PPC and AMP .
RNA-directed RNA polymerase, catalytic domain (RNA-dir_pol_PSvirus)
Type: Domain

This entry represents the catalytic domain of the RNA-directed RNA polymerase from all positive-strand RNA eukaryotic viruses with no DNA stage.

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .
RNA-directed RNA polymerase, catalytic domain, bacteriophage (RNA-dir_Rpol_cat_phage)
Type: Domain

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents the catalytic (palm) domain from the RNA-containing bacteriophage enzymes.
RNA-directed RNA polymerase, reovirus (RNA-dir_pol_reovirus)
Type: Domain

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents the Reoviridae family of dsRNA viruses.
RNA-directed RNA polymerase, negative-strand RNA virus (RNA-dir_pol_NSvirus)
Type: Domain

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry corresponds to a relatively conserved segment of 147 - 180 aa of RdRp or its catalytic subunit.
The proteins in this family are: RNA polymerase PB1 subunits of Orthomyxoviruses and RNA polymerases (L proteins) of Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.
Birnavirus RNA-directed RNA polymerase, palm domain (Birnavirus_RdRp_palm)
Type: Domain

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents the "palm" domain of RdRp from Birnavirus. These proteins lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RNA-directed RNA polymerases . The catalytic motifs are arranged in a permuted order, thus, adopting a unique active site topology .
Brix domain (Brix)
Type: Domain

Analysis of the Brix (biogenesis of ribosomes in Xenopus) protein leaded to the identification of a region of 150-180 residues length, called the Brix
domain, which is found in six protein families: one archaean family (I) including hypothetical proteins (one per genome); and five eukaryote families, each named according to a representative member and including close homologues of this prototype: (II) Peter Pan (D. melanogaster) and SSF1/2 (S.cerevisiae); (III) RPF1 (S. cerevisiae); (IV) IMP4 (S. cerevisiae); (V) Brix (X.laevis) and BRX1 (S. cerevisiae); and (VI) RPF2 (S.cerevisiae).

Typically, a protein sequence belonging to the Brix domain superfamily contains a highly charged N-terminal segment (about 50 residues) followed by a single copy of the Brix domain and another highly charged C-terminal region (about 100 residues). The archaean sequences have two unique characteristics: (1) the charged regions are totally absent at the N terminus and are reduced in number to about 10 residues at the C terminus; and (2) the C-terminal part of the Brix domain itself is minimal. Two eukaryote groups have large insertions within the C-terminal region: about 70 residues in the group III and about 120 in the group II. Biological data for some proteins in this family suggest a role in ribosome biogenesis and rRNA binding .
Immunoglobulin-like domain (Ig-like_dom)
Type: Domain

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 .
NACHT nucleoside triphosphatase (NACHT_NTPase)
Type: Domain

The NACHT domain is a 300 to 400 residue predicted nucleoside triphosphatase (NTPase) domain, which is found in animal, fungal and bacterial proteins. The NACHT domain has been named after NAIP, CIITA, HET-E and TP1. It is found in association with other domains, such as the CARD domain (

), the DAPIN domain (

), the HEAT repeat (

), the WD repeat (

), the leucine-rich repeat (LRR) or the BIR repeat (

) .

The NACHT domain consists of seven distinct conserved motifs, including the ATP/GTPase specific P-loop, the Mg(2+)-binding site (Walker A and B motifs, respectively) and five more specific motifs. The unique features of the NACHT domain include the prevalence of 'tiny' residues (glycine, alanine or serine) directly C-terminal of the Mg(2+)-coordinating aspartate in the Walker B motif, in place of a second acidic residue prevalent in other NTPases. A second acidic residue is typically found in the NACHT-containing proteins two positions downstream. Furthermore, the distal motif VII contains a conserved pattern of polar, aromatic and hydrophobic residues that is not seen in any other NTPase family .
Expansin/pollen allergen, DPBB domain (Expansin/allergen_DPBB_dom)
Type: Domain

This entry represents a N-terminal domain that has a Barwin-like double psi β-barrel structure(DPBB). It is found in proteins like expasin and pollen allergens. The major timothy grass pollen allergen Phl p 1 is one of the most potent and frequently recognised environmental allergens .
6-pyruvoyl tetrahydropterin synthase/QueD family (6-PTP_synth/QueD)
Type: Family

6-Pyruvoyl tetrahydrobiopterin synthase (PTPS) catalyses the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP . The functional enzyme is a hexamer of identical subunits. A transition metal binding site formed by the three histidine residues 23, 48 and 50 is present in each subunit, and bound Zn(II) is responsible for the enzymatic activity. Site-directed mutagenesis of each of these three histidine residues results in a complete loss of metal binding and enzymatic activity .

Member this entry is also 6-carboxy-5,6,7,8-tetrahydropterin synthase (QueD) that catalyses the conversion of 7,8-dihydroneopterin triphosphate (H2NTP) to 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) and acetaldehyde .
Expansin, cellulose-binding-like domain (Expansin_CBD)
Type: Domain

Expansins are secreted proteins of 25 to 27 Kd that were isolated first from young cucumber seedling and subsequently from other plant tissues. Expression of expansin genes correlates with growth of cells. Increase in expansin content also occurs during fruit ripening. Expansins act on the cell wall to promote its extensibility. The model for its mechanism of action postulates that expansins break non-covalent bonds between cell-wall polysaccharides, thereby permitting pressure dependent expansion of the cell .

Group-I pollen allergens of grasses have limited but significant sequence homology to expansin. These proteins are the main causative agent of hay fever and seasonal asthma induced by grass pollen. Extracts containing group-I allergens are also active in loosening cell-walls. Group-I pollen allergens and related proteins in vegetative tissues have been classified as beta-expansins, whereas the earlier discovered expansins are now referred as α-expansins .

Expansin-like proteins are also found in some fungi. In Trichoderma reesei an expansin-like protein (Cel12A) acts as a glycoside hydrolase on xyloglucan and 1-4 beta-glucan. These hydrolytic actions differ from the action by expansins, which induce wall extension by a non-hydrolytic mechanism .

Expansins consist of two domains closely packed and aligned so as to form a long, shallow groove with potential to bind a glycan backbone of ~10 sugar residues. The N-terminal cysteine-rich domain has distant sequence similarity to family-45 endoglucanases (EG45-like domain). The ~90-residue C-terminal domain may function as a cellulose-binding domain (CBD). It is composed of eight β-strands assembled into two antiparallel β-sheets. The two β-sheets are at slight angles to each other and form a β-sandwich similar to the Ig fold .

This entry represents the expansin C-terminal CBD-like domain.