SII-SWORD/CoKE huggingface dataset:
GCN5-related N-acetyltransferase 5-like domain (GCN5-like_dom)
Type: Domain

This entry represents a domain found towards the C-terminal end of GCN5-related N-acetyltransferase 5, chloroplastic from Arabidopsis thaliana, an enzyme with dual specificity triggering both N-alpha-acetylation (NTA) and epsilon-lysine acetylation (KA) . This domain is also found C-terminal in GCN5-like protein acetyltransferase Rv2170 from Mycobacterium tuberculosis, which is involved in the post-translational regulation of the central metabolic enzyme isocitrate dehydrogenase 1 (ICDH-1) through lysine acetylation .

Proteins in this entry have a conserved region similar to the C-terminal region of the Drosophila melanogaster (Fruit fly) hypothetical protein FR47 (

). This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands.
PAS fold-2 (PAS_2)
Type: Domain

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [1]. The PAS fold appears in archaea, eubacteria and eukarya.
PAS fold-3 (PAS_fold_3)
Type: Domain

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya, and is involved in a variety of functions within sensory proteins promoting protein-protein interactions, signal transfer or as a stimuli sensor . The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL , FAD in the redox potential sensor NifL , and a 4-hydroxycinnamyl chromophore in photoactive yellow protein . Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
PAS fold-4 (PAS_4)
Type: Domain

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs . The PAS fold appears in archaea, eubacteria and eukarya. This domain recognises differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
SLC35B1-4/HUT1 (SCL35B1-4/HUT1)
Type: Family

This family represents a group of nucleotide sugar transporters (NSTs) that belong to the SLC35 family of solute carriers and their function is highly conserved from simple eukaryotes, fungi and parasites to plants and mammals, including the nucleotide sugar transporters SLC35B1-4 from human and HUT1 and YEA4 from yeast . Members of this family localize at the Golgi apparatus and/or the endoplasmic reticulum (ER) and exhibit different substrate specificities, for instance, YEA4 has specificity for UDP-N-acetylglucosamine, which is localized in the ER and required for chitin synthesis . SLC35B1 from human has been identified as a ATP:ADP antiporter that catalyses the exchange of ATP and ADP across the ER membrane where it imports ATP from the cytosol to the ER lumen and exports ADP in the opposite direction. SLC35B1 regulates ER energy metabolism, probably as part of a calcium-dependent ER to cytosol low energy response axis and it also provides ATP to ER chaperones required for proper protein folding and trafficking in the ER . HUT1, SLC35B1 orthologues, play a more general role in ER homeostasis .
SMP-30/Gluconolactonase/LRE-like region (SGL)
Type: Domain

This family describes a region that is found in proteins expressed by a variety of eukaryotic and prokaryotic species. These proteins include various enzymes, such as senescence marker protein 30 (SMP-30, also known as regucalcin

), gluconolactonase (

) and luciferin-regenerating enzyme (LRE,

). SMP-30 is a gluconolactonase with low activity towards other sugar lactones, including gulonolactone and galactonolactone. It is known to hydrolyse diisopropyl phosphorofluoridate in the liver, and has been noted as having sequence similarity, in the region described in this family, with PON1 (

) and LRE.
Adenosine/AMP deaminase N-terminal (A_deaminase_N)
Type: Domain

This domain is found toward the N terminus of the Adenosine/AMP deaminase domain (

) in metazoan proteins such as the Cat eye syndrome critical region protein 1 and its homologues.
DNA polymerase B exonuclease, N-terminal (DNApol_B_exo_N)
Type: Domain

This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (

).
Peptidase M9, collagenase, N-terminal domain (Peptidase_M9_N_dom)
Type: Domain

Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation, which is usually zinc but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophilic role.

Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .

This domain is found in the N-terminal region of microbial collagenase metalloproteases, which belong to peptidase family M9. Microbial collagenases have been identified from bacteria of both the Vibrio and Clostridium genuses. Collagenase is used during bacterial attack to degrade the collagen barrier of the host during invasion. Collagen cleavage occurs at an Xaa+Gly in Vibrio bacteria and at Yaa+Gly bonds in Clostridium collagenases.
RyR/IP3R Homology associated domain (RIH_assoc-dom)
Type: Domain

This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1, 4, 5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels . There seems to be no known function for this domain .
Helicase, SWF/SNF/SWI type, bacterial (Helicase_SWF/SNF/SWI_bac)
Type: Domain

This domain is found in bacterial proteins of the SWF/SNF/SWI helicase family to the N terminus of the SNF2 family N-terminal domain (

) and together with the Helicase conserved C-terminal domain (

). The function of the domain is not clear .
Viral methyltransferase, C-terminal domain (Virgavirus_MeTrfase_C)
Type: Domain

This domain is found to the C terminus of the viral methyltransferase domain (

) in single-stranded-RNA positive-strand viruses with no DNA stage in the Virgaviridae family.
Sfi1 spindle body (Sfi1_dom)
Type: Domain

This is a domain of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organising centres.
Pleckstrin-like, plant (PH_pln)
Type: Domain

This domain describes a pleckstrin homology (PH)-like region found in several plant proteins, including VAN3-binding protein from Arabidopsis thaliana (also known as FORKED1), a component of the auto-regulatory loop which enables auxin canalisation by recruitment of the PIN1 auxin efflux protein to the cell membrane .
Ribonuclease R winged-helix domain (RNase_R_HTH_12)
Type: Domain

This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Coat protein, C-terminal, Carmoviral (Coat_prot_C_Carmovir)
Type: Domain

This domain is found to the C terminus of the

domain in Carmoviruses. The coat protein of the Turnip crinkle virus (TCV; Tombusviridae) is a suppressor of RNA silencing and is required for cell to cell movement in its host . The plant cellular trafficking machinery could hijack functional viral proteins to permit cell-to-cell movement of RNA silencing . The 3'-proximal coat protein is coded by ORF4 .
EcoEI R protein C-terminal domain (EcoEI_R_C_dom)
Type: Domain

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzymes include EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity .
Geminivirus AC4/5, conserved domain (Gemini_AC4/5_cons-dom)
Type: Domain

This domain is found in replication initiator (Rep) associated proteins such as AC5 in the Geminivirus/Begomovirus.
Herpesvirus thymidine kinase, C-terminal (Herpes_TK_C)
Type: Domain

This domain is found towards the C terminus in Herpesvirus Thymidine kinases.
Luteovirus RNA polymerase P1-P2/replicase (Luteo_Rpol_P1-P2)
Type: Domain

This domain is found in RNA-dependent RNA polymerase P1-P2 fusion/replicase proteins in plant Luteoviruses.
Methyltransferase small, N-terminal (Mtase_sm_N)
Type: Domain

This domain is found to the N terminus of the methyltransferase small domain (

) in bacterial proteins .
Nucleoside triphosphatase I, C-terminal (NPHI_C)
Type: Domain

This entry represents the C-terminal domain of Nucleoside triphosphatase I (NPH1), specific to the family Poxviridae . It is usually found associated with the helicase conserved C-terminal domain (

).

NPH1 serves two roles in transcription. It is a DNA-dependent ATPase required for providing the needed energy to achieve the termination of early transcripts. In response to the termination signal UUUUUNU, this protein uses the mechanism known as forward translocation to releases transcripts. wich consists of moving the transcription elongation complex downstream on the DNA template . Simultaneously, this protein acts by itself as a polymerase elongation factor .
Nontoxic nonhaemagglutinin C-terminal (Nontoxic_nonhemagglutn_C)
Type: Domain

Bacteria of the Clostridium genus produce protein neurotoxins, which are complexes consisting of neurotoxin (NT), haemagglutinin (HA), nontoxic nonhaemagglutinin (NTNH), and RNA . The domain described here is found at the C terminus of the NTNH component.
Ribonucleotide reductase class II vitamin B12-dependent, N-terminal domain (RNR_2_N)
Type: Domain

This domain is found to the N terminus of the ribonucleotide reductase barrel domain (

). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) .
Sucrose-phosphatase, C-terminal (SPP_C)
Type: Domain

This is the sucrose-phosphatase (S6PP or SPP) C-terminal domain as found in plant sucrose phosphatases. These enzymes irreversibly catalyse the last step in sucrose synthesis following the formation of Sucrose-6-Phosphate via sucrose-phosphate synthase (SPS).
Voltage-dependent calcium channel, alpha-2/delta subunit, conserved region (VDCC_a2/dsu)
Type: Domain

Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins . The activity of this pore is modulated by four tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits.

Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels.

This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2/delta subunits to the N terminus of a Cache domain (

).
Myelin transcription factor 1 (Myelin_TF)
Type: Domain

This domain is found in the myelin transcription factor 1 (MYT1) of chordates. MYT1 contains C2HC zinc finger domains (

) and is expressed in developing neurons of the central nervous system where it is involved in the selection of neuronal precursor cells .
Baculovirus Vp91, capsid protein, N-terminal (BaculoV_Vp91_N)
Type: Domain

This domain is a C2HC BV-type zinc finger found at the N terminus of the viral capsid protein 91 (VP91) from baculoviruses such as nucleopolyhedrovirus . Vp91 plays multiple roles in the baculovirus life cycle and is essential for nucleocapsid assembly and for efficient establishment of per os infection. It contains a C2HC zinc finger with the consensus sequence C-x(5)-
C-x(n)-H-x(6)-C. The C2HC BV-type zinc finger may perform a pivotal role in the association of Vp91 with other per os infectivity factors (PIFs) .
Vaccinia virus D10, N-terminal (Vaccinia_D10_N)
Type: Domain

This domain is found at the N-terminal end of Protein D10 from Vaccinia virus, also known as mRNA-decapping protein OPG122, and similar sequences from poxvirus. The VD10 protein is probably essential for virus replication and is often found to the N terminus of a NUDIX hydrolase domain.

Previous studies indicated that the vaccinia virus D10 protein, which is conserved in all sequenced poxviruses, participates in the rapid turnover of host and viral mRNAs. D10 contains a motif present in the family of Nudix/MutT enzymes, a subset of which has been shown to enhance mRNA turnover in eukaryotic cells through cleavage of the 5' cap (m7GpppNm-). The D10 protein possesses an intrinsic activity that liberates m7GDP from capped RNA substrates. Furthermore, point mutations in the Nudix/MutT motif abolished decapping activity. D10 has a strong affinity for capped RNA substrates of lengths of 24-309 nt were decapped efficiently. The poxviruses represent the only virus family shown to encode a Nudix hydrolase-decapping enzyme. The activity of the decapping and capping enzymes, accelerate mRNA turnover and helps to eliminate competing host mRNAs allowing stage-specific synthesis of viral proteins . D10 preferentially targets spliced mRNAs and since all viral genes are intronless and host over viral transcripts . Acceleration of the turnover of cellular transcripts promotes the shutoff of host protein synthesis and therefore diminish the magnitude of antiviral response .
POTRA domain, FtsQ-type (POTRA_FtsQ_type)
Type: Domain

FtsQ/DivIB bacterial division proteins (

) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane β-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts .
Polypeptide-transport-associated, ShlB-type (Polypept-transport_assoc_ShlB)
Type: Domain

The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (

). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal β-barrel channel .
Disaggregatase-related (Disaggr-rel)
Type: Domain

The members of this family are disaggregatases and several hypothetical proteins of the archaeal genus Methanosarcina. Disaggregatases cause aggregates to separate into single cells and contain parallel β-helix repeats. Also see

.
GBS Bsp-like (GBS_Bsp-like)
Type: Repeat

This repeat is found in a number of Streptococcus proteins including some hypothetical proteins and Bsp. Bsp is a protein of group B Streptococcus (GBS) which might control cell morphology .
ATP-dependent RNA helicase HrpB, C-terminal (RNA_helicase_ATP-dep_HrpB_C)
Type: Domain

This domain is found near the C terminus of bacterial ATP-dependent helicases such as HrpB.
C-methyltransferase (MeTrfase_14)
Type: Domain

This domain is found in bacterial C-methyltransferase proteins, often together with other methyltransferase domains such as

or

.
UDP-glucose 4-epimerase CapD, C-terminal domain (CapD_C)
Type: Domain

This domain is found to the C terminus of the

domain in the polysaccharide biosynthesis enzyme CapD from some bacteria. CapD epimerises UDP-galactose to UDP-glucose .
Sporulation stage II protein D, amidase enhancer LytB N-terminal (SpoIID/LytB_N)
Type: Domain

This domain is found in the stage II sporulation protein SpoIID. SpoIID is necessary for membrane migration as well as for some of the earlier steps in engulfment during bacterial endospore formation . The domain is also found in amidase enhancer proteins. Amidases, like SpoIID, are cell wall hydrolases .
VIT domain (VIT)
Type: Domain

The inter-alpha-trypsin inhibitor (ITI) family is composed of protease inhibitors that are assembled from two precursor proteins: a light chain and different homologous heavy chains (ITIHs). Originally identified as plasma inhibitors, recent data indicate that ITI plays a role in extracellular matrix stabilisation and in prevention of tumour metastasis .

Two domains are conserved in all known ITIHs, the vault protein inter-alpha- trypsin (VIT) domain and a von Willebrand type A (vWA) domain. The VIT domain is less widespread than the vWA domain and is not genetically mobile. Therefore, it can be regarded as the characteristic domain of the ITIH family. The VIT domain is approximately 135 amino acids long. Its N-terminal part contains a pattern of hydrophobic residues, interrupted by a conserved arginine. The C terminus is best characterised by its conserved aromatic residues. In the central part, an acidic amino acid resides between two basic residues .
Wall-associated receptor kinase (WAK)
Type: Domain

This domain is found together with the eukaryotic protein kinase domain

in plant wall-associated receptor kinases (WAKs) and related proteins. WAKs are serine-threonine kinases which might be involved in signalling to the cytoplasm and are required for cell expansion .
TiaS, FLD domain (TiaS_FLD)
Type: Domain

This is the FLD domain found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS . TiaS is an ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) . This modified base specifically recognises AUA codons. TiaS consists of four domains, the TCKD domain at the N-terminal followed by the FLD domain, an OB fold domain and a zinc ribbon domain (ZRD) domain at the C-terminal . The FLD domain is responsible for agmantine binding .
DNA polymerase epsilon, catalytic subunit A, C-terminal (DNA_pol_e_suA_C)
Type: Domain

This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to

and

.
Squalene epoxidase (Squalene_epoxidase)
Type: Domain

This domain is found in squalene epoxidase (SE) and related proteins which are found in taxonomically diverse groups of eukaryotes and also in bacteria. SE was first cloned from Saccharomyces cerevisiae (Baker's yeast) where it was named ERG1. It contains a putative FAD binding site and is a key enzyme in the sterol biosynthetic pathway . Putative transmembrane regions are found to the protein's C terminus.
Signal recognition particle, SRP72 subunit, RNA-binding (Signal_recog_part_SRP72_RNA-bd)
Type: Domain

The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes . SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor . Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukaryotic complex: SRP19 and SRP54 .

This entry represents the RNA binding domain of the SRP72 subunit. This domain is responsible for the binding of SRP72 to the 7S SRP RNA .
Aflatoxin regulatory protein (AflR)
Type: Domain

This domain is found in the aflatoxin regulatory protein (AflR) and related fungal sequences. AflR is involved in the regulation of the biosynthesis of aflatoxin in the fungal genus Aspergillus . It occurs together with the fungal Zn(2)-Cys(6) binuclear cluster domain (

).

Aflatoxins belong to a family of decaketides that are produced as secondary metabolites by Aspergillus flavus and Aspergillus parasiticus . The aflatoxin biosynthetic pathway involves several enzymatic steps that appear to be regulated by the aflR genes in A. flavus and A. parasiticus. AflR encodes a protein that contains a cysteine-rich motif. Several fungal transcriptional activator proteins contain this motif, which binds DNA in a zinc-dependent fashion (occurs in fungal transcriptional regulatory proteins) .