SII-SWORD/CoKE huggingface dataset:
PRP8 domain IV core (PRP8_domainIV)
Type: Domain

This entry represents Prp8 domain IV, which adopts a RNase H like fold within its core structure but with little sequence similarity. Pre-mRNA-splicing factor 8 (Prp8), a spliceosome protein, interacts directly with the splice sites and branch regions of precursor-mRNAs and spliceosomal RNAs associated with catalysis of the two steps of splicing. Catalysis of RNA cleavage by RNase H-like proteins involves a two-metal mechanism in which adjacently-bound divalent magnesium ions promote hydrolysis by activation of a water nucleophile and stabilization of the transition-state. However, the Prp8 domain IV contains only one of the canonical metal-binding sites and the coordinating side chains are spatially conserved with respect to Mg2+-coordinating residues within the RNase H fold .
Plasmodium repeat (Plasmodium_rpt)
Type: Repeat

This repeat is found in plasmodia. This entry contains two copies of the repeat. The function of these proteins is unknown.
RNA polymerase Rpo13 subunit HTH domain (RNA_pol_Rpo13)
Type: Domain

This domain is found in archaea, and is about 40 amino acids in length. It has a single completely conserved residue E that may be functionally important. The domain is a 'helix-turn-helix' (HTH) domain in the Rpo13 subunit of the archaeal RNA polymerase . This domain is involved in downstream DNA binding, and the entire subunit has also been implicated in contacting transcription factor II B.
Spherulation-specific family 4 (Spherulin4)
Type: Family

This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length. There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein.
SLED domain (SLED)
Type: Domain

The SLED (Scm-Like Embedded Domain) domain is a double-stranded DNA binding domain found in Scml2 which is a member of the Polycomb group of proteins involved in epigenetic gene silencing .
Beta-mannosyltransferase (BMT1)
Type: Family

This entry represents a group of fungal beta-mannosyltransferase that is involved in cell wall biosynthesis . For example, in Candida albicans, BMT1-4 enzymes act stepwise to add beta-mannoses onto cell-wall phosphopeptidomannan (PPM). While Bmt5 and Bmt6 are involved in the addition of the first and third beta-mannoses to phospholipomannan (PLM), respectively . Furthermore, in Saccharomyces cerevisiae, BMT5 and BMT6 are responsible for methylation of uridine residues in the 25S rRNA .
Mediator complex, subunit Med12, catenin-binding (Mediator_Med12_catenin-bd)
Type: Domain

This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. It is found in the C-terminal region of the mediator of RNA polymerase II transcription subunit 12. Both development and carcinogenesis are driven by signal transduction within the canonical Wnt/beta-catenin pathway through both programmed and unprogrammed changes in gene transcription. Beta-catenin physically and functionally targets this PQL (proline-, glutamine-, leucine-rich) region of the Med12 subunit of Mediator to activate transcription. The beta-catenin transactivation domain binds directly to isolated Med12 and intact Mediator both in vitro and in vivo, and Mediator is recruited to Wnt-responsive genes in a beta-catenin-dependent manner.
Mediator complex, subunit Med12, LCEWAV-domain (Mediator_Med12_LCEWAV)
Type: Domain

This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. The function of this particular region of the Mediator subunit Med12 is not known, but there is a conserved sequence motif: LCEWAV, from which the name derives.
UHRF1, tandem tudor domain (TTD_dom)
Type: Domain

TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognises H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3) .
Mannan-binding protein (MVL)
Type: Domain

This domain family is found in bacteria, and is approximately 40 amino acids in length, There is a single completely conserved residue G that may be functionally important. The domain occurs in two types of proteins. In mannan binding proteins , it forms a homodimeric molecule which complexes into a homo-octamer. In thiamidases it occurs without repeats but in the presence of other domains. MVL is distinct amongst other oligomannoside binding proteins in that it exhibits specificity for certain tetrasaccharides. Each molecule of MVL has four distinct carbohydrate binding sites.
Putative metal-binding domain of cation transport ATPase (ATPase-cat-bd)
Type: Domain

This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with

,

,

. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Domain of unknown function DUF3592 (DUF3592)
Type: Domain

This entry represents a β-barrel domain ubiquitously found, primarily in bacteria, but also in archaea and in kinetoplastids. Proteins in this family are typically between 150 and 242 amino acids in length. The domain is often found in integral membrane proteins.
Protein of unknown function DUF3593 (DUF3593)
Type: Family

This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 98 and 228 amino acids in length. There is a conserved LHG sequence motif.
Fibrinogen alpha C domain (Fibrinogen_aC)
Type: Domain

This domain family is found in eukaryotes, and is approximately 70 amino acids in length, and the family is found in association with

. This domain is the C-terminal domain of fibrinogen in mammals. The domain lies in the C-terminal half of the alpha C region in these proteins. The function of the domain is that of intramolecular and intermolecular interactions to form fibrin.
Stage V sporulation protein AA (SporV_AA)
Type: Domain

This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up.
Alfin, N-terminal (Alfin_N)
Type: Domain

This entry represents the N-terminal domain found in Alfin family members.

The Alfin family includes PHD finger protein Alfin1 and Alfin1-like proteins. They contain a conserved N domain at the N terminus, a PHD finger domain with conserved C4HC3 residues at the C terminus and a variable V region between the two conserved domains . Alfin1 is a histone-binding component that specifically recognises H3 tails trimethylated on 'Lys-4' (H3K4me3), which marks transcription start sites of virtually all active genes . Alfin1-like proteins have been shown to play roles in root growth and abiotic stress response .
Min27-like integrase, DNA-binding domain (Min27-like_integrase_DNA_bind)
Type: Domain

This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 90 amino acids in length. The family is found in association with

. It is likely that this domain acts to bind DNA.
DNA polymerase III subunit tau, DnaB-binding domain IV (DNA_pol3_tau_IV)
Type: Domain

This domain found in bacterial proteins, and is approximately 80 amino acids in length. It is found in association with

. domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding domain IV and all of the alpha-interacting domain V are unique to tau.
ChsH2, rubredoxin-like zinc ribbon domain (ChsH2_Znr)
Type: Domain

This domain is found in the probable enoyl-CoA hydratase alpha subunit from Thermomonospora curvata (ChsH2) and similar archaeal and bacterial proteins. ChsH2 is likely to be involved in bile acid degradation. The C-terminal region of this protein is organised into two domains: an N-terminal zinc finger domain with a three-stranded antiparallel β-sheet and an N-terminal α-helix (this entry), and a C-terminal domain with an oligonucleotide/oligosaccharide binding (OB)-fold that consists of a five-stranded β-barrel (

) .

Other members of this group of proteins are Geobacter metallireducens Benzoylsuccinyl-CoA thiolase subunit BbsA, a component of the BbsAB thiolase complex, which catalyses the thiolytic cleavage of (S)-2-benzoylsuccinyl-CoA to succinyl-CoA and benzoyl-CoA, the final step of anaerobic toluene metabolism , and Methanothermococcus thermolithotrophicus HMGCS, an enzyme complex comprising the thiolase and 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase, that catalyses the second reaction in the mevalonate pathway-the exergonic condensation of acetoacetyl-CoA and acetyl-CoA to HMG-CoA .

The domain is duplicated in

from M.tuberculosis. The structure of

from Saccharolobus solfataricus reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this entry and a C-terminal OB fold domain . Zinc is chelated by the four conserved cysteines in the alignment.
RST domain (RST)
Type: Domain

The RST (for RCD1 SRO TAF4) domain is a plant-specific domain found in WWE- PARPs (poly(ADP-ribose) polymerase) and TAF4s (TBP-Associated Factor 4), a component of several multimeric protein complexes including primarily the general transcription factor TFIID involved in transcriptional initiation. The RST domain is a protein-protein interaction domain suggested to be critical for the interaction with several, mostly plant-specific transcription factors .

The RST domain structure has a unique helical arrangement composed of four α helices flanked by disordered termini. The four-helix fold of the RST domain organizes in an open, hydrophobic L-shape with room for catching the ligand . A strong conservation of a large number of aliphatic amino acids in the N- and C-termini of the RST domain, with a conserved tyrosine in the middle of the domain and two conserved positively charged amino acids in the second half of the domain, is striking . This entry represents the RST domain.
White spot syndrome virus structural envelope protein Vp28 (WSSV_Vp28)
Type: Domain

This family of proteins is found in viruses. Proteins in this family are approximately 210 amino acids in length. There is a conserved NNT sequence motif. These proteins are structural envelope proteins in viruses. This is the β barrel C-terminal domain. There is a protruding N-terminal domain which completes the proteins. Three of four envelope proteins in Shrimp white spot syndrome virus share sequence homology with each other and are present in this family - VP24, VP26 and VP28. VP19 is the other major envelope protein but shares no sequence homology with the other proteins. These proteins are essential for entry into cells of the crustacean host.
Prohormone convertase enzyme (Proho_convert)
Type: Domain

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with

,

. There are two completely conserved residues (Y and D) that may be functionally important. This protein is the C-terminal domain of a prohormone convertase enzyme which targets hormones in dense core secretory granules. This C-terminal tail domain is the domain responsible for targeting these dense core secretory granules. The domain adopts an α helical structure .
Chromosome passenger complex (CPC) protein INCENP N-terminal (INCENP_N)
Type: Domain

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N-terminal domain is the domain involved in formation of this three helical bundle.
I-kappa-kinase-beta NEMO binding domain (IKKbetaNEMObind)
Type: Domain

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with

. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO.
TSG101 and ALIX binding domain of CEP55 (EABR)
Type: Domain

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR.
Restriction endonuclease, type II, NotI (Resctriction_endonuc_II_NotI)
Type: Domain

This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 341 amino acids in length. There is a conserved CPF sequence motif. The type IIP restriction enzyme, NotI, is a homodimer that recognises the 8 bp DNA sequence 5'-GC/GGCCGC-3' and cleaves both strands of DNA to create 5', 4 base cohesive overhangs.
Nup358/RanBP2 E3 ligase domain (IR1-M)
Type: Domain

This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with

,

,

. There are two conserved sequence motifs: TFFC and EDF. Nup358/RanBP2 is a nucleoporin involved in ubiquitination of many different protein targets from various cellular pathways. It complexes with Ubc9, SUMO-1 and RanGAP1 to perform this function. This is the ligase domain which binds to Ubc9.
D212, catalytic domain (D212_cat_dom)
Type: Domain

This family of proteins represented by Sulfolobus spindle-shaped virus (Ragged Hills) ORF D212; the structure of which has been reported . The structure of D212 clearly reveals a type II restriction endonuclease fold and identifies the hallmark PD-(D/E)XK catalytic motif that is spatially conserved in this nuclease superfamily. This fold and its associated catalytic residues
are also found in nucleases, where they play roles in DNA replication, repair, recombination, and other processes requiring nuclease activity. The function of D212 in the phage replication cycle remains unknown, it is speculated to be a Holliday junction cleavage .
Fungal calcium binding protein (CBP)
Type: Domain

This domain is found in eukaryotes, and is approximately 60 amino acids in length. There is a single completely conserved residue C that may be functionally important. This is a calcium binding domain from the fungal protein CBP (calcium binding protein). This protein is a virulence factor with unknown virulence mechanisms. CBP complexes as a highly intertwined homodimer. Each monomer is comprised of four α helices which adopt the saposin fold, characteristic of a protein family that binds to membranes and lipids.
Sulfolobus virus, coat protein, C-terminal (Sulfobus_virus_coat_C)
Type: Domain

This domain family is found in viruses, and is approximately 70 amino acids in length. It is the C-terminal of a coat protein in sulfolobus viruses.
Tuberculin-active protein (Tuberculin)
Type: Domain

This entry represents a domain found in the tuberculin-active protein from Mycobacterium tuberculosis .
Domain of unknown function DUF3597 (DUF3597)
Type: Domain

The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. It is found in proteins from bacteria, eukaryotes and viruses. The function of this domain is not known.
Biogenesis factor required for ATP synthase 1-like, DUF3598 (BFA1-like_DUF3598)
Type: Domain

This entry represents a domain predominantly found in proteins from cyanobacteria and plants, including Biogenesis factor required for ATP synthase 1 (BFA1,

) from Arabidopsis thaliana and other uncharacterised proteins. BFA1 promotes the assembly of the CF1 subcomplex of the chloroplast ATP synthase by specifically interacting with the gamma and beta subunits. This protein consists of two distinct β-barrels: a typical β-barrel with ten β-sheets and one α-helix and an atypical one, oriented perpendicularly, with nine β-sheets and two α-helices; and shows structural similarity with the lipocalin superfamily .
ARF GTPase-activating protein GIT1, C-terminal (GIT1_C)
Type: Domain

This entry represents the C-terminal domain of the ARF GTPase-activating protein GIT1. GIT1 is an ArfGAP and scaffolding protein regulating cell adhesion and migration . To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C-terminal and the LD motifs of paxillin. The C-terminal folds into a four helix bundle.
Domain of unknown function DUF3600 (DUF3600)
Type: Domain

This domain is found at the C terminus of the putative ECF-type sigma factor negative effector. Proteins in this entry are approximately 230 amino acids in length.
Domain of unknown function DUF3601 (DUF3601)
Type: Domain

This domain family is found in bacteria, and is approximately 80 amino acids in length.
Immune evasion protein (M04gp34-like)
Type: Family

The proteins in this family are related to the m04 encoded protein gp34 of pathogenic microorganisms such as Murid herpesvirus 1. m06 and m152 genes are expressed earlier in the intracellular replication phases of these microorganism' life cycles. They function to inhibit MHC-1 loading and export. gp34 is theorized to prevent immune reactions from NK cells which would ordinarily recognise and attack cells lacking MHC .
U1 small nuclear ribonucleoprotein of 70kDa N-terminal (U1snRNP70_N)
Type: Domain

This domain is about 90 amino acids in length and is found at the N terminus of U1 small nuclear ribonucleoprotein 70kDa (U1-70K), which is part of the U1 snRNP (snRNP) complex. U1 snRNP recognises the 5' splice site within precursor messenger RNAs and initiate the assembly of the spliceosome for intron excision.

The N-terminal region of U1-70K extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition .
Protein of unknown function DUF3602 (DUF3602)
Type: Family

This domain family is found in eukaryotes, and is typically between 78 and 89 amino acids in length. This entry include protein Par32 from Saccharomyces cerevisiae. Par32 is hyperphosphorylated after treatment with rapamycin in a TAP42-dependent manner . It is also involved in resistance to cisplatin .
Putative amidoligase enzyme (Amidoligase_2)
Type: Family

This family of proteins are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighbourhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes) .
Methylene-tetrahydrofolate reductase C-terminal-like (DUF5981)
Type: Domain

This entry represents a domain of unknown function, which contains 8 conserved cysteine residues that might form a metal binding site.
Turkey astrovirus capsid protein (Astro_capsid_p)
Type: Family

This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains.
Protein of unknown function DUF3604 (DUF3604)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 621 and 693 amino acids in length.
YoaR-like, putative peptidoglycan binding domain (YoaR-like_PG-bd)
Type: Domain

This domain is found associated with the L,D-transpeptidase domain

in the uncharacterised protein YoaR from Bacillus subtilis and similar bacterial proteins. The structure of this domain has been solved and shows a mixed α-β fold composed of nine β strands and four α helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain.
Splicing factor 3A subunit 1, conserved domain (SF3A1_dom)
Type: Domain

This domain is found in eukaryotes, and is typically between 212 and 238 amino acids in length. It is found in association with

. There are two completely conserved residues (W and H) that may be functionally important. It is found in the subunit 1 of mammalian splicing factor SF3A, which is involved in converting the U2 snRNP into its active form during pre-mRNA splicing .
Telomere-associated protein Rif1, N-terminal (Rif1_N)
Type: Domain

This domain is found in N-terminal of the telomere-associated protein,Rif1. In budding yeast, Rif1 is Recruited to telomeres by interaction with the C terminus of RAP1 is recruited to telomeres by interaction with the C terminus of RAP1 and negatively regulates telomere length by preventing telomere elongation or promoting degradation of the telomere ends . In mammals, Rif1 is required for checkpoint mediated arrest of cell cycle progression in response to DNA damage during S-phase (the intra-S-phase checkpoint) .
Myogenic determination factor 5 (Myf5)
Type: Domain

This domain is found in eukaryotes, is approximately 70 amino acids in length, and contains a conserved CSD sequence motif. It is found in association with

,

. This domain is found in Myogenic factor 5 (Myf5) and Myoblast determination protein 1 (MyoD1). Myf5 is responsible for directing cells to the skeletal myocyte lineage during development . Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function .
RAVE complex protein Rav1 C-terminal (Rav1p_C)
Type: Domain

This domain family is found in the C-terminal region of the protein Rav1 , a component of the RAVE (regulator of the ATPase of vacuolar and endosomal membranes) complex. Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits .
Fragile X messenger ribonucleoprotein 1-like, C-terminal core (FMR1-like_C_core)
Type: Domain

This entry represents the core C-terminal region of the fragile X messenger ribonucleoprotein 1 (FMR1) and its paralogues fragile X-related proteins 1/2 (FXR1/2). These proteins have different regions at their very C terminus. The Glutamine-arginine rich region facilitates protein interactions . Proteins containing this domain contain two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs .

Fragile X messenger ribonucleoprotein 1 (FMR1), fragile X-related 1 protein (FXR1) and fragile X-related 2 protein (FXR2) are members of a small family of RNA-binding proteins that are involved the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs, playing a crucial role in neuronal development and synaptic plasticity . The proteins contain two KH domains and a RGG box that are characteristic motifs in RNA-binding proteins as well as nuclear localization and export signals.