SII-SWORD/CoKE huggingface dataset:
Microspherule protein, N-terminal domain (MCRS_N)
Type: Domain

This domain is found in plants and higher eukaryotes, and is the N-terminal region of micro-spherule proteins which repress the transactivation activities of Nrf1 (p45 nuclear factor-erythroid 2 (p45 NF-E2)-related factor 1) . In conjunction with DIPA the full-length protein acts as a transcription repressor . The exact function of this domain is not known.
Anaphase-promoting complex subunit 5 domain (Apc5_dom)
Type: Domain

This entry represents a domain found in Apc5 (anaphase-promoting complex subunit 5).

Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multisubunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Tetratricopeptide repeat protein 19 is a mitochondrial protein required for formation of the mitochondrial complex III .

Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction . The N terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC . This region of the Apc5 member proteins carries a TPR-like motif.
Abortive infection protein-like, C-terminal domain (Abi-like_C)
Type: Domain

This domain is found at the C terminus of the Lactococcus lactis abortive infection protein Abi-859,

. This protein confers bacteriophage resistance .
L-2-amino-thiazoline-4-carboxylic acid hydrolase (ATC_hydrolase)
Type: Family

This family of enzymes catalyses the conversion of L-2-amino-delta2-thiazoline-4-carboxylic acid (L-ATC) to N-carbamoyl-L-cysteine . They cleave the carbon-sulphur bond in the ring structure of L-ATC to produce N-carbamoyl-L-cysteine .
HEAT repeat associated with sister chromatid cohesion protein (Cohesin_HEAT)
Type: Repeat

This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B . HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble.
Septum formation-related domain (Septum_form)
Type: Domain

This domain is found in a protein which is predicted to play a role in septum formation during cell division and in uncharacterised proteins.
Uridine kinase (Uridine_kinase_)
Type: Family

This entry represents a family of uridine kinase proteins .

Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyses the following reaction:

ATP + Uridine = ADP + UMP

A cDNA for uridine kinase from mouse brain was found which encodes a protein of 277 amino acids. A truncated form of the cDNA was expressed in Escherichia coli, and shown to display uridine kinase activity and to readily form a tetramer, the most active form of the wild-type enzyme. Sequence analysis has identified three ATP-binding site consensus motifs. The predicted secondary structure, and sequence comparison with kinases of known structure, is consistent with uridine kinase having the α/β core nucleotide-binding fold common to many kinases .
Nucleoporin NSP1/NUP62 (NSP1/NUP62)
Type: Family

NSP1 functions as a component of the nuclear pore complex (NPC). The 55-60 MDa NPC is composed of at least 31 different subunits. NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors .

NUP62 is a component of the p62 complex, composed of NUP62, NUP54, and the isoform p58 and isoform p45 of NUPL1 . The p62 complex is an assembly of glycoproteins localised near the central gated channel of the nuclear pore complex.
F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily (ATP_synth_OSCP/delta_N_sf)
Type: Homologous_superfamily

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

The subunits called delta in bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit,

). The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B' (chloroplasts) .

This superfamily represents the N-terminal six α-helix bundle domain of the OSCP/delta subunit .
Lumazine-binding domain (Lumazine-bd_dom)
Type: Domain

The lumazine-binding domain is about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. Riboflavin synthase alpha chain (RS-alpha), which binds two molecules of Lum, has two perfect copies of this motif, while lumazine protein (LumP), which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, yellow fluorescent protein (YFP), which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.

The lumazine-binding domain of RS-alpha forms two Greek-key folds with the topology BBHBBBHB, where most of the substrate binding sites are located in β-strands (B) 4 and 5 and in helix (H) 2 .
Small ribosomal subunit protein uS7, archaeal (Ribosomal_uS7_arc)
Type: Family

This entry represents the archaeal uS7 ribosomal proteins.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Ribulose-phosphate 3-epimerase (Ribul_P_3_epim)
Type: Family

Ribulose-phosphate 3-epimerase (

) (also known as RPE, pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Ralstonia eutropha (Alcaligenes eutrophus) two copies of the gene coding for PPE are known , one is chromosomally encoded

, the other one is on a plasmid

. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.
Putative NAD(P)H nitroreductase YdjA-like (YdjA-like)
Type: Family

This group consists of putative NAD(P)H nitroreductases represented by Ydja .
PhoU domain (PhoU_dom)
Type: Domain

PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle . The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect; suggesting that the protein has some secondary function . The crystal structure of PHOU_AQUAE reveals two similar coiled-coil PhoU domains, each forming a three-helix bundle .
Chemotaxis protein methyltransferase CheR (Chemotaxis_MeTrfase_CheR)
Type: Family

Protein methyltransferase CheR binds to a specific sequence at the C-termini of some chemotaxis receptors and from this tethering position methylates neighbouring receptor molecules .
Fatty acid synthase alpha subunit, yeast (FAS_alpha_yeast)
Type: Family

Fatty acid synthetase catalyses the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. The alpha subunit contains domains for: acyl carrier protein, 3-oxoacyl-[acyl-carrier-protein] reductase, and 3-oxoacyl-[acyl-carrier-protein] synthase .
Histidine triad hydrolase, Hint-type (HIT_Hint)
Type: Family

HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literature into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, which consists of diadenosine polyphosphate hydrolases, and the GalT branch, consisting of specific nucleoside monophosphate transferases. Further sequence analysis reveals several new, closely related, yet uncharacterised subgroups.
Phosphatidylcholine synthase Pcs (PcS)
Type: Family

Phosphatidylcholine synthase PcS condenses choline with CDP-diglyceride to produce phosphatidylcholine and CMP .
.
ATPase, V0 complex, subunit 116kDa, eukaryotic (V-type_ATPase_116kDa_su_euka)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

This entry represent eukaryotic V-ATPase 116kDa subunit (also known as subunit a). V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex . V-ATPase 116kDa subunit is part of the integral membrane V0 complex of vacuolar ATPase and is essential for assembly and catalytic activity . V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.
Muconolactone isomerase domain (MLI_dom)
Type: Domain

This entry represents a domain that covers almost the entire length of muconolactone delta-isomerase - an enzyme that forms a homodecameric complex , which catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway (

). The domain is also found duplicated in some proteins.
Purine-cytosine permease Fcy2/21/22 (Pur-cyt_permease_Fcy2/21/22)
Type: Family

This entry represents a family of purine-cytosine permeases from bacteria and fungi, including Fcy2/21/22 from budding yeasts and fcyB from Emericella nidulans . Fcy2 is a purine-cytosine permease (PCP) that mediates the active transport of purines and cytosine. Fcy21 and Fcy22 show protein sequence similarity to Fcy2, but cannot substitute for its function .
Cytochrome c-type biogenesis protein CcmB, bacteria (Cyt_c_CcmB_bac)
Type: Family

This entry represents cytochrome c-type biogenesis protein CcmB (HelB) from bacteria. CcmB is the product of one of a cluster of ccm genes that are necessary for cytochrome c biosynthesis in bacteria and is required for the export of haem to the periplasm .
Probable 3-phenylpropionic acid transporter-like (HcaT-like)
Type: Family

This is a group of permeases mainly found in bacteria, and includes probable 3-phenylpropionic acid transporter HcaT from Escherichia coli , and uncharacterised transporter YwbF from Bacillus subtilis.
Azaguanine-like transporters, bacteria and archaea type (Azg-like_bact_archaea)
Type: Family

This entry includes azaguanine-like (Azg-like) transporters mostly from bacteria and archaea, including AdeP/AdeQ from E. coli, PbuG/PbuO from Bacillus subtilis and PlAzg1 from Paenibacillus larvae subsp. larvae. AdeP/AdeQ are adenine permeases , PbuG/PbuO are guanine/hypoxanthine permeases , while PlAzg1 is a nucleobase transporter that transports adenine, hypoxanthine, xanthine and uracil .
Cell shape-determining protein MreD, proteobacterial type (MreD_proteobac)
Type: Family

The MreD (murein formation D) protein is involved in bacterial cell shape determination . Most rod-shaped bacteria depend on MreB and RodA to achieve either a rod shape or some other non-spherical morphology such as coil or stalk formation. MreD is encoded in an operon with MreB, and often with RodA and PBP-2 as well. It is highly hydrophobic (therefore somewhat low-complexity) and highly divergent, and therefore cannot always be identified on the basis of sequence similarity.

This entry represents the proteobacterial MreD proteins.
PucC protein (PucC)
Type: Family

The PucC protein, also known as bacteriochlorophyll delivery (BCD), is required for high-level transcription of the PUC operon, essential for formation of the light harvesting complex B800-850 (LH2) of Rhodobacter capsulatus as well as deliver bacteriochlorophyll a to nascent LH2 complexes.
Phosphatidylglycerophosphatase A (PgpA)
Type: Family

This family represents a family of bacterial phosphatidylglycerophosphatases (

), known as PgpA. It appears that bacteria possess several phosphatidylglycerophosphatases, and thus, PgpA is not essential in Escherichia coli .
Putative phosphatidylglycerophosphatase (Put_PGPase)
Type: Family

This family includes uncharacterised proteins like YutG from Bacillus subtilis (

), and other proteins described as putative phosphatidylglycerophosphatases.
Ancillary SecYEG translocon subunit YfgM (YfgM)
Type: Family

YfgM is a subunit of the ancillary SecYEG translocon that may mediate protein transfer from the SecYEG translocon to the periplasmic chaperone network via its periplasmic C-terminal region . It may coordinate stress responses across the inner membrane via a dynamic protein-protein interaction network inside and outside of the membrane .
Hydroxypyruvate isomerase-like (HyI-like)
Type: Family

This family includes hydroxypyruvate isomerase Hyi from Escherichia coli , glyoxylate induced protein YgbM (also known as 2-oxo-tetronate isomerase) and other uncharacterised proteins.
Glyoxalase ElbB (ElbB)
Type: Family

ElbB, also known as enhancing lycopene biosynthesis protein 2 (Elb2), may be involved in the early steps of isoprenoid biosynthesis . It has glyoxalase activity .
Stress response protein YjbJ (YjbJ)
Type: Family

This entry represents a group of bacterial stress response proteins.
Transcription repressor NadR (NadR)
Type: Family

In Bacillus subtilis, NadR represses transcription of the nadBCA and nifS-nadR operons in the presence of nicotinic acid. It also binds to DNA upstream of the niaP gene and probably regulating it. This protein may bind nicotinic acid . NadR is also known as NiaR.
Membrane-bound lytic murein transglycosylase A (MltA)
Type: Family

Membrane-bound lytic murein transglycosylase A is a murein-degrading enzyme. It may play a role in recycling of muropeptides during cell elongation and/or cell division .
Ferric binding protein (Ferric-bd)
Type: Family

This entry represents a group of ferric binding and related proteins. They are probably part of a periplasmic ABC transporter complex involved in Fe3+ (ferric) ion import, and include FbpA , FutA1 and FutA2 .
UbiA prenyltransferase domain containing protein 1 (UBIAD1)
Type: Family

UbiA prenyltransferase domain-containing protein 1 is a prenyltransferase that mediates the formation of menaquinone-4 (MK-4), a vitamin K2 isoform present at high concentrations in the brain, kidney and pancreas . Also included in this family are 1,4-dihydroxy-2-naphthoate octaprenyltransferase MenA and 2-carboxy-1,4-naphthoquinone phytyltransferase from bacteria.
Uncharacterised protein C2orf42 (C2orf42)
Type: Family

This family consists of uncharacterised proteins.
C1GALT1/C1GALT1-specific chaperone 1 (C1GALT1/C1GALT1_chp1)
Type: Family

This group of proteins consist of glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferases (C1GALT1) and C1GALT1-specific chaperone 1 (C1GALT1C1). C1GALT1 helps to generate the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins .

C1GALT1-specific chaperone 1 (C1GALT1C1) was first described as a glycosyltransferase, however, it has no transferase activity and rather acts as a chaperone probably acts as a specific molecular chaperone assisting the folding/stability of C1GALT1 .
Chitobiosyldiphosphodolichol beta-mannosyltransferase ALG1-like (ALG1-like)
Type: Family

ALG1 (Asparagine-linked glycosylation protein 1) proteins participate in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. They are also involved in assembling the dolichol-pyrophosphate-GlcNAc(2)-Man5 intermediate on the cytoplasmic surface of the ER .

Defects in human ALG1 are the cause of congenital disorder of glycosylation type 1K (CDG1K). CDGs are characterised by under-glycosylated serum proteins. These multisystem disorders present with a wide variety of clinical features, such as disorders of the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. .

Glycosylation and growth of Alg1-deficient PRY56 yeast cells, showing a temperature-sensitive phenotype, could be restored by the human wild-type allele .
DNA-binding protein inhibitor (DNA-bd_prot-inh)
Type: Family

Transcription factors containing basic-helix-loop-helix (bHLH) domains interact to regulate differentiation in a number of cellular systems, including myogenesis, neurogenesis and haematopoiesis . The DNA-binding activity of these proteins is mediated via the basic region of the bHLH domain, and is dependent upon formation of homo- and/or heterodimers by these transcription factors.

The Id family of proteins (whose members include Id1, Id2, Id3 and the Drosophila homologue emc) contain a HLH-dimerisation domain but lack the DNA-binding basic region. Formation of heterodimers between these proteins and bHLH domain-containing transcription factors abolishes the DNA-binding ability of the latter, thus inhibiting their activity .

Id proteins can inhibit the differentiation of progenitors of different cell types, promoting cell-cycle progression, delaying cellular senescence, and facilitating cell migration. These properties enable them to play important roles in stem cell maintenance, vasculogenesis, tumorigenesis and metastasis, the development of the immune system, and energy metabolism .
BLOC-3 complex member HPS1 (HPS1)
Type: Family

Defects in human HPS1 are the cause of Hermansky-Pudlak syndrome type 1 (HPS1). Hermansky-Pudlak syndrome (HPS) is an often-fatal autosomal recessive disease in which albinism, bleeding, and lysosomal storage result from defects of diverse cytoplasmic organelles: melanosomes, platelet dense bodies, and lysosomes .

Human HPS1 is a transmembrane protein component of the BLOC-3 complex, a complex that acts as a guanine exchange factor (GEF) for RAB32 and RAB38, promotes the exchange of GDP to GTP, converting them from an inactive GDP-bound form into an active GTP-bound form. The BLOC-3 complex plays an important role in the control of melanin production and melanosome biogenesis and promotes the membrane localization of RAB32 and RAB38 .
Nuclear pore complex protein (Nucleoporin)
Type: Family

Nucleoporins (NUP) are the components of the nuclear pore complex (NPC). They can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. The nuclear pore complex constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. NPC is composed of at least 31 different subunits.

This family includes nucleoporin Nup121 (Pom121) , Nup153 and Nup124 among others.
Fatty acyl-CoA reductase (FAR)
Type: Family

This is a fatty acyl-CoA reductase family that can catalyse the reduction of fatty acyl-CoA to fatty alcohols .
Trichome birefringence-like, C-terminal domain (TBL_C)
Type: Domain

This entry represents a group of plant proteins from the PC-Esterase family including Arabidopsis thaliana PMR5 and a group of plant freezing resistance/cold acclimatization proteins typified by Arabidopsis thaliana ESKIMO1 (also known as XOAT1) . The PC-Esterase family has features that are both similar and different from the canonical GDSL/SGNH superfamily . The members of this family are predicted to have Acyl esterase activity and predicted to modify cell-surface biopolymers such as glycans and glycoproteins . The plant family with PMR5, XOAT1, TBL3 etc have an N-terminal C rich potential sugar binding domain followed by the PC-Esterase domain .

In Arabidopsis, XOAT1 catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions . Its role is essential for the production of functional xylem vessels . It functions as a negative regulator of cold acclimation, and mutations in the ESK1 gene provides strong freezing tolerance .