SII-SWORD/CoKE huggingface dataset:
Protein ea8.5-like superfamily (ea8_5-like_sf)
Type: Homologous_superfamily

This entry includes Protein ea8.5 from Bacteriophage lambda (

) and similar sequences mostly from tailed bacteriophages and bacterial prophages. It ranges from around 45 to 90 residues in length and is associated with nucleic acid binding function, playing an essential role in the inhibition of the initiation of DNA synthesis in the phage host. NMR analysis shows it adopts a hybrid homeodomain/zinc-finger fold, which suggests a regulatory role .
Vitamin uptake-like sensor (VUPS)
Type: Domain

This is an integral membrane sensory domain related to the queuosine precursor transporter (

, found in YhhQ protein from E. coli). This domain, named Vitamin uptake-like sensor (VUPS), is found in a variety of bacteria in combination with PAS (

,

), GGDEF (

), and EAL (

) domains, and with histidine sensor kinases (

) .
Lysosomal alpha-mannosidase-like, central domain (Man2a1-like_dom)
Type: Domain

This domain is found in Lysosomal alpha-mannosidase from Rattus norvegicus (Man2a1) and similar proteins from animals and plants. Man2a1 catalyses the first committed step in the biosynthesis of complex N-glycans. It controls the conversion of high mannose to complex N-glycans, the final hydrolytic step in the N-glycan maturation pathway . Man2a1 belongs to the glycoside hydrolase family 38 (GH38).
RRN6, beta-propeller (RRN6_beta-prop)
Type: Domain

This entry represents the β-propeller domain of Rrn6 which is part of the palm (or module I in ) of the CF which interacts with Rrn11 . Rrn6 is the fungal homologue of TAF1C . Members of this entry are specific to fungi.

RNA polymerase I-specific transcription-initiation factor Rrn6 is a component of a multisubunit core transcription factor, essential for the initiation of rDNA transcription by Pol I . The DNA-bound core factor (CF) resembles a right hand holding the DNA molecule between the fingers and the palm, with the thumb pointing toward Pol I. The palm is composed of the N-terminal regions of Rrn11 and Rrn6, the thumb is composed of the C-terminal of Rrn11 while the fingers and knuckles are composed of Rrn7 and the C-terminal half of Rrn6, respectively .
RRN6, K-rich C-terminal domain (Rrn6_K-rich)
Type: Domain

This is the C-terminal K-rich domain from RNA polymerase I-specific transcription initiation factor Rrn6 and related proteins found in fungi.

RNA polymerase I-specific transcription-initiation factor Rrn6 is a component of a multisubunit core transcription factor, essential for the initiation of rDNA transcription by Pol I . The DNA-bound core factor (CF) resembles a right hand holding the DNA molecule between the fingers and the palm, with the thumb pointing toward Pol I. The palm is composed of the N-terminal regions of Rrn11 and Rrn6, the thumb is composed of the C-terminal of Rrn11 while the fingers and knuckles are composed of Rrn7 and the C-terminal half of Rrn6, respectively .
RRN6, helical bundle domain (RRN6_HB)
Type: Domain

This entry represents the helical bundle domain (also referred to as the headlock domain) from RNA polymerase I-specific transcription initiation factor RRN6. This helical domain is found C-terminal to the β-propeller (

), that wraps around Rrn7 and is part of module II of the core factor (CF) .

RNA polymerase I-specific transcription-initiation factor Rrn6 is a component of a multisubunit core transcription factor, essential for the initiation of rDNA transcription by Pol I . The DNA-bound core factor (CF) resembles a right hand holding the DNA molecule between the fingers and the palm, with the thumb pointing toward Pol I. The palm is composed of the N-terminal regions of Rrn11 and Rrn6, the thumb is composed of the C-terminal of Rrn11 while the fingers and knuckles are composed of Rrn7 and the C-terminal half of Rrn6, respectively .
Rrn7/TAF1B, C-terminal cyclin domain (Rrn7_cyclin_C)
Type: Domain

This is the C-terminal cyclin domain of Rrn7 from yeast and the orthologues from animals and plants TAF1B .

Rrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains. In Rrn7, the cyclin domains interact with both Rrn6 and Rrn11 and form the fingers of the core factor which resembles a right hand. N-terminal regions of both Rrn11 and Rrn6 compose the palm, the thumb is composed by the C-terminal of Rrn11 and the knuckles consist of the C-terminal half of Rrn6.
Carboxysome Shell Carbonic Anhydrase, catalytic domain (CsoSCA_cat)
Type: Domain

Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localised in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains: an N-terminal domain composed primarily of four α-helices (

); a catalytic domain containing a tightly bound zinc ion and a C-terminal domain with weak structural similarity to the catalytic domain . This entry represents the catalytic domain, consisting of a central five-stranded mixed β-sheet with two helices flanking one side of the sheet and one helix flanking the other side .
Rrn7/TAF1B, N-terminal cyclin domain (Rrn7_cyclin_N)
Type: Domain

This is the first cyclin domain (cyclin I) from yeast Rrn7 and its orthologues from animals and plants TAF1B .

Rrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains. In Rrn7, the cyclin domains interact with both Rrn6 and Rrn11 and form the fingers of the core factor which resembles a right hand. N-terminal regions of both Rrn11 and Rrn6 compose the palm, the thumb is composed by the C-terminal of Rrn11 and the knuckles consist of the C-terminal half of Rrn6.
Exosome complex component RRP40, N-terminal domain (RRP40_N)
Type: Domain

Exosome complex component RRP40 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal β-sandwich hybrid domain, a central S1 domain and a C-terminal KH domain (

). This entry represents the N-terminal domain of RRP40 mainly from mammals .
Probable sensor domain DacZ_T (DacZ_T)
Type: Domain

This is a probable sensor domain found at the N-terminal of archaeal diadenylate cyclases, which are typically followed by the DAC (

) domain. It is distantly related to PK_C (

) and DacZ_N (

).
L544-like, nucleotidyltransferase domain (L544-like_NTransf)
Type: Domain

This is the nucleotidyltransferase domain found in uncharacterised proteins from Mimiviridae, such as L544 from Acanthamoeba polyphaga mimivirus (

,

).
Probable sensor domain DacZ_P (DacZ_P)
Type: Domain

This is a probable sensor domain found at the N-terminal of bacterial diadenylate cyclases, which are typically followed by the DAC (

) domain. It is distantly related to PK_C ([interpro: IPR015795) and it consists of four α-helices and five β-strands according to structure predictions.
L544-like, helical domain (L544-like_helical)
Type: Domain

This is the helical domain found at the C-terminal of the uncharacterised protein L544 from Acanthamoeba polyphaga (

,

), which is thought to be a nucleotidyltransferase, and similar sequences from Mimiviridae.
Probable sensor domain DacZ_A (DacZ_A)
Type: Domain

This is a probable sensor domain found at the N-terminal of archaeal diadenylate cyclases, which are typically followed by the DAC (

) domain. It may consist of four α-helices and four β-strands according to structure predictions. DacZ_A is distantly related to PK_C (

), DacZ_N (

) and DACZ_P (

).
RNA-directed RNA polymerase L, thumb ring domain, bunyaviral (L_thumb_ring_bunyavir)
Type: Domain

This entry represents the thumb ring domain of RNA-directed RNA polymerase L from Bunyavirus La Crosse (L) (

,

) and similar sequences from Bunyavirales. This domain adopts an α/β structure that is structurally similar to the influenza PB2 N1 and N2 domains .
KRR1 small subunit processome component, second KH domain (KRR1-like_KH2)
Type: Domain

This is the second K homology domain (KH2) found in KRR1 small subunit processome component from Saccharomyces cerevisiae and similar eukaryotic and archaeal sequences.

Ribosomal RNA assembly protein KRR1 is required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly in Saccharomyces cerevisiae . In Schizosaccharomyces pombe it is known as Mis3 .
KRR1 small subunit processome component, second KH domain, eukaryotes (KRR1-like_KH2_euk)
Type: Domain

This is the second K homology domain (KH2) found in KRR1 small subunit processome component from Saccharomyces cerevisiae and similar eukaryotic sequences.

Ribosomal RNA assembly protein KRR1 is required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly in Saccharomyces cerevisiae . In Schizosaccharomyces pombe it is known as Mis3 .
KRR1 small subunit processome component, first KH domain, eukaryotes (KRR1-like_KH1_euk)
Type: Domain

This is the first K homology domain (KH1) found in KRR1 small subunit processome component from Saccharomyces cerevisiae and similar eukaryotic sequences.

Ribosomal RNA assembly protein KRR1 is required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly in Saccharomyces cerevisiae . In Schizosaccharomyces pombe it is known as Mis3 .
Probable sensor domain DACNV (DACNV)
Type: Domain

This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by the DAC (

) domain. DACNV consists of a compact core formed by seven β-strands and two or three α-helices, according to structure predictions. It is found in various phyla, including acidobacteria, actinobacteria, bacteroidetes, cyanobacteria and planctomycetes.
Probable sensor domain DACND (DACND)
Type: Domain

This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases which are typically followed by the DAC (

). It may consist of four α-helices and three β-strands according to structure predictions. This domain is mainly found in thermodesulfobacteriotes.
Kinetochore null protein 2-like domain (Knl-2-like_dom)
Type: Domain

This entry represents a domain found towards the C-terminal of Kinetochore null protein 2 from Caenorhabditis elegans (Knl-2) and similar sequences from related species. It shows an all-helical structure. It is normally found associated with

.
Probable sensor domain DACNG (DACNG)
Type: Domain

This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by a DACNH (

) and DAC (

) domains. This domain may have five α-helices and four β-strands according to structure predictions.
Probable sensor domain DACNH (DACNH)
Type: Domain

This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases which is typically followed by the DAC (

) domain. This domain may consist of two α-helices and seven β-strands. In deltaproteobacteria, this domain is preceded by the DACND (

) or DACNG domains (

).
Probable sensor domain DACNK (DACNK)
Type: Domain

This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by the DAC (

) domain. This domain is mainly found in actinobacteria and cyanobacteria; structure predictions suggest that this domain may consist of five α-helices and five-eight β-strands.
Disabled homolog 1/2, sulfatide-binding motif (DAB1/2_SBM)
Type: Conserved_site

This region is found at the N-terminal end of human Disabled homolog 2 (DAB2) and similar sequences predominantly found in vertebrates. DAB2 is an adaptor protein involved in endocytosis, cell surface receptor turnover, and cell signalling. The membrane binding properties of this protein depend on its sulfatide-binding motifs (SBM, represented by this entry), which display a helical conformation . This region is N-terminal to the PID domain (

).
Lysine-specific demethylase 6A/B-like, GATA-like (KDM6A_B-like_GATAL)
Type: Domain

This entry represents the Zn-coordinated GATA-like (GATAL) domain of human Lysine-specific demethylase 6A/B and similar animal sequences. This region seems to be sensitive to redox environment. It is involved in substrate binding .

Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY (also known as KMD6C) .
Disabled, phosphotyrosine-binding domain (Dab_PTB)
Type: Domain

Disabled (Dab) is a cytosolic adaptor protein, which binds to the cytoplasmic tails of lipoprotein receptors, such as ApoER2 and VLDLR, via its phosphotyrosine-binding domain (PTB) domain . The Dab PTB domain has a preference for non phosphorylated tyrosine within an NPxY motif. Additionally, the Dab PTB domain, which is structurally similar to PH domains, binds to phosphatidylinositol phosphate 4,5 bisphosphate in a manner characteristic of phosphoinositide binding PH domains.

PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This entry is part of the Dab-like subgroup
Lysine-specific demethylase 6A/B-like, C-terminal helical domain (KDM6A_B-like_C-hel)
Type: Domain

This entry represents the C-terminal helical domain of human Lysine-specific demethylase 6A/B and similar animal sequences. This domain is localised adjacent the JmjC domain (

).

Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY (also known as KMD6C) .
Peptidyl-prolyl cis-trans isomerase CYP38-like, PsbQ-like domain (CYP38_PsbQ-like)
Type: Domain

Peptidyl-prolyl cis-trans isomerase CYP38 from Arabidopsis is required for the assembly and stabilisation of PSII . It consists of an N-terminal helical bundle and a C-terminal cyclophilinβ-barrel (

).

This entry represents the N-terminal helical bundle found in Cyp37/38 from Arabidopsis and similar proteins from plants and cyanobacteria. This domain establishes strong interactions with the C-terminal domain to avoid the access of the cyclophilin domain to other proteins .
Cyanate hydratase, N-terminal domain (CYNS_N)
Type: Domain

Cyanate hydratase (also known as cyanate lyase) catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate . It consists of an N-terminal five-helix bundle domain that shows structural similarity to DNA-binding HTH domains and a C-terminal catalytic domain, which has a unique fold . This entry represents the N-terminal domain.
RRP4, S1 domain (RRP4_S1)
Type: Domain

Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of an N-terminal β-sandwich hybrid domain (

), a central S1 domain and a C-terminal KH domain (

). This entry represents the S1 RNA binding domain, which has an OB fold .

The exosome plays a central role in 3' to 5' RNA processing and degradation in eukaryotes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the 'S1 pore structure' .
DNA-directed RNA polymerase subunit beta', hybrid domain (RpoC_hybrid)
Type: Domain

This entry represents a hybrid domain found in DNA-directed RNA polymerase subunit beta' (RPOC) from Thermus thermophilus and similar sequences mainly found in Deinococcus .
Cyanobacterial TRADD-N associated 2, transmembrane domain (CyanoTRADDas_TM)
Type: Domain

This is a domain with two transmembrane helices predicted to function as a pore-forming effector and found mainly in bacterial conflict systems .
RTX toxin, C-terminal repeat (RtxA_C)
Type: Repeat

This entry represents a short repeat found near the C-terminal of some RTX toxins such as MARTX (

) . AlphaFold models suggest that this repeat forms a β-solenoid structure. These repeats contain a GXGXD motif in each repeat which is similar to that found in the RTX calcium-binding nonapeptide repeat (

). This suggests that these repeats may also be required for translocation via the type I secretion system .
Rubicon, PI3K-binding domain (RUBC_PIKBD)
Type: Domain

This is the PI3K-binding domain (PIKBD) localised in the middle region of Rubicon (

), rubicon-like proteins such as PACER (

) and homologues from animals. Rubicon is a potent negative regulator of autophagy through the interaction with Rab7-GTP . This domain is predicted to have disordered and helical regions .
26S proteasome non-ATPase regulatory subunit 1/RPN2, N-terminal domain (PSMD1_RPN2_N)
Type: Domain

This entry represents the N-terminal helical domain of 26S proteasome non-ATPase regulatory subunit 1 (PSMD1) and 26S proteasome regulatory subunit RPN2. It adopts a rod-like structure .
Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical (RuBisCO_activase_AAA_helical)
Type: Domain

This domain is found in Ribulose bisphosphate carboxylase/oxygenase activase from Nicotiana tabacum (RuBisCO activase) and similar proteins from plants and cyanobacteria. This enzyme facilitates the removal of the sugar phosphate inhibitors of RuBisCO, the enzyme that catalyses the fixation of atmospheric CO2 in photosynthesis. This protein is organised into an N-terminal domain, followed by a AAA module and a 23-residue C-terminal extension. The AAA module is composed of an α/β and an α-helical subdomains. This entry covers part of the α-helical subdomain and the C-terminal extension .
Rotavirus non-structural protein 35, N-terminal domain (Rota_NS35_N)
Type: Domain

Rotavirus non-structural protein 35 (NS35, also known as NSP2) is a basic protein which possesses RNA-binding, and helix-destabilising activities in addition to nucleoside and 5' RNA triphosphatase (NTPase/RTPase) and nucleoside-diphosphate (NDP) kinase-like activities . NS35 forms a functional octamer which is essential for genome replication and formation of viroplasms . This is the N-terminal domain, which contains basic residues, that in addition to the basic residues in the C-terminal helix, are important for sequence-independent RNA binding of NS35 . This domain also has conserved cysteine residues which form disulfide that might be relevant for NS35 activity .
Rubrerythrin, rubredoxin-like domain (RUBY_RBDX)
Type: Domain

Rubrerythrin (RUBY) is a fusion protein containing an N-terminal diiron-binding domain (

) and a C-terminal rubredoxin-like domain. RUBY may play a role in oxidative stress.

This entry represents the rubredoxin-like domain of RUBY, reverse rubrerythrin 1/2 from Clostridium acetobutylicum (RRBR1/2) and Nigerythrin from Desulfovibrio vulgaris . RRBRs function as the terminal component of an NADH peroxidase when using NADH:rubredoxin oxidoreductase (NROR) as the electron transport intermediary from NADH to RRBRs and play an important role in the oxidative stress defence system of C. acetobutylicum .
Roquin 1/2-like, ROQ domain (Roquin_1_2-like_ROQ)
Type: Domain

This domain is found in Roquin-1/2 from humans and in other eukaryotic RING-E3 ubiquitin ligases and transferases. These paralogous proteins Roquin-1/2 recruit the deadenylation and decapping machineries to initiate mRNA degradation. They play a central role in repressing autoimmunity. The ROQ domain, highly conserved, is required for RNA binding and shows a mostly helical structure with a small three-stranded β-sheet. It bears a winged helix-turn-helix motif, which is involved in the binding of constitutive decay elements-containing stem-loop mRNAs .
DNA-binding protein Rv2175c, wHTH domain (Rv2175c_wHTH)
Type: Domain

This entry represents the N-terminal wHTH domain of Rv2175c (

) from Mycobacterium tuberculosis and related bacterial proteins. It was shown that this domain bind DNA . The C-terminal domain

may play a regulatory role.
Rv3651-like, C-terminal domain (Rv3651-like_C)
Type: Domain

This domain is found in Rv3651 from Mycobacterium tuberculosis (

) and similar proteins from Actinobacteria. Rv3651 is composed of three domains. This entry represents the C-terminal domain, a PAS domain that shows a central antiparallel β-sheet consisting of five β-strands .
Ribonuclease D, C-terminal HRDC domain (RNAseD_HRDC_C)
Type: Domain

Ribonuclease D is a bacterial 3'-5' exonuclease that acts on tRNA. It contributes to the 3' maturation of several stable RNAs . It consists of a catalytic domain (

) and two α-helical domains at the C-terminal that closely resemble the HRDC domain seen in RecQ-family helicases. This entry represents the second HRDC domain from RNAse D. The first one is included in

.
Adenylate cyclase, C-terminal, yeast (CYAA_C)
Type: Domain

Yeast adenylate cyclase (CYAA/CYR1) is required for cAMP production and cAMP-dependent protein kinase signalling. It is a scaffold protein for Ras2-Ira interaction . This entry represents the C-terminal domain which contains a second Ras binding site (the first resides in the LRR region) which is involved in a GTP-independent weak interaction between Ras and a complex of adenylate cyclase and Srv2 protein . These two Ras binding sites are required for normal Ras2 downregulation .
Ryanodine receptor, junctional solenoid domain (RYDR_Jsol)
Type: Domain

This entry represents a region found in ryanodine receptors composed of α-helical ARM repeats . This region has been termed the Junctional solenoid region (Jsol) .
RNase E/G, thioredoxin-like domain (RNase_E_G_thioredoxin-like)
Type: Domain

Both RNase E and its homologue RNase G are endoribonucleases that play central roles in RNA processing. RNase E shows two globular domains. This entry represents the smaller domain, which shows a thioredoxin-like fold .
Small ribosomal subunit protein uS5m, N-terminal domain (Ribosomal_uS5m_N)
Type: Domain

This entry represents an extension segment found at the N-terminal of mitochondrial 28S Small ribosomal subunit protein uS5m . This region lines a part of the mRNA entry path and connects the 28S subunit body to the head forming a latch across the mRNA channel entrance .
C-X-C motif chemokine 16 domain (CXCL16_dom)
Type: Domain

This entry represents the CXC chemokine-like domain found near the N-terminal of the CXCL16 protein, which acts as a scavenger receptor on macrophages and specifically binds to OxLDL (oxidized low density lipoprotein) .
N-acetylmuramoyl-L-alanine amidase Cwp6-like, N-terminal domain (Cwp6-like_N)
Type: Domain

This domain is found in the putative N-acetylmuramoyl-L-alanine amidase Cwp6 from Clostridioides difficile (

) and similar proteins from Clostridia. Cwp6, which is involved in cell wall remodelling, consists of five domains: an N-terminal domain, a trimer of CWB2 (

) and a C-terminal domain (

).

This entry represents the N-terminal domain, which locates at the bottom of the molecule, folds into a seven-stranded β-barrel with one α-helix and with two additional short β-strands .