SII-SWORD/CoKE huggingface dataset:
Hydrophobic abundant protein (HAP) (HAP)
Type: Family

This entry represents the homologues of Sporulation-specific hydrophobic abundant protein (

).

Expression of Hydrophobic Abundant protein is thought to be developmentally regulated and possibly involved in spherule cell wall formation .
Fushi tarazu, N-terminal (FTZ_N)
Type: Domain

This region contains the important motif (LXXLL) necessary for the interaction of FTZ with the nuclear receptor FTZ-F1. FTZ is thought to represent a category of LXXLL motif-dependent co-activators for nuclear receptors.
Large ribosomal subunit protein uL6, N-terminal (Ribosomal_uL6_N)
Type: Domain

This entry represents the N-terminal domain of Large ribosomal subunit protein eL6 and similar eukaryotic proteins.

Large ribosomal subunit protein uL6 was previously known as L6. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites .

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 .
Arc-like DNA binding domain (Arc_DNA-bd_dom)
Type: Domain

Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel β-sheet to recognise bases in the major groove .
DNA-directed RNA polymerases I, II, and III subunit RPABC3 (RPABC3)
Type: Family

This family includes DNA-directed RNA polymerases I, II, and III subunit RPABC3 (also known as Rpb8), an essential subunit common to the three RNA polymerases, pol I, II and III . Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits.
RNA polymerase, Rpb5, N-terminal (RNA_pol_Rpb5_N)
Type: Domain

Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP;

) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (

) .

This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers α/β/α . The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure . This module is important for positioning the downstream DNA.
Anti sigma-E protein RseA, N-terminal (Anti-sigma_E_RseA_N)
Type: Domain

Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters . The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress.
Anti sigma-E protein RseA, C-terminal (Anti-sigma_E_RseA_C)
Type: Domain

Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters . The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress.
RNA polymerase subunit Rpb4/RPC9 (Rpb4/RPC9)
Type: Family

This entry includes RNA polymerase II subunit Rpb4 and its paralogue, RPC9 (also known as Rpc17 in budding yeasts), a subunit of RNA polymerase III . The Rpb4 and Rpb7 subunits of yeast RNA polymerase II form a heterodimeric complex essential for promoter-directed transcription initiation. The Rpb4-Rpb7 complex is not required for stable recruitment of polymerase to active preinitiation complexes, suggesting that Rpb4-Rpb7 mediates an essential step subsequent to promoter binding . RPC9 may be involved in the recruitment of pol III by the preinitiation complex .
Statherin (Statherin)
Type: Family

Statherin is a 43-residue peptide, secreted by parotid and submandibular glands. Statherin functions biologically to inhibit the nucleation and growth of calcium phosphate minerals. The N terminus of statherin is highly charged, the glutamic acids of which have been shown to be important in the recognition hydroxyapatite . Moreover, statherin and its C-terminal fragments inhibit the growth of anaerobic bacteria from the oral cavity .
RNA polymerase Rpb7-like , N-terminal (Rpb7-like_N)
Type: Domain

Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpa43 of RNAP I, Rpc8/Rpc25 of RNP III, and RpoE of archaeal RNAP. Rpb7 binds to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation and plays a part in transcription, mRNA transport and DNA repair . In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA . The N terminus of Rpb7 and homologues has a SHS2 domain that is involved in protein-protein interaction .
Yif1 family (Yif1_fam)
Type: Family

Yif1 (Yip1 interacting factor) is an integral membrane protein required for membrane fusion of ER derived vesicles . It also plays a role in the biogenesis of ER derived COPII transport vesicles .
Cgr1-like (Cgr1-like)
Type: Family

Cgr1 is involved in nucleolar integrity and is required for processing pre-rRNA for the 60S ribosome subunit. In Saccharomyces cerevisiae, this protein is conserved and contributes to compartmentalisation of nucleolar constituents . Cgr1 is a small hydrophilic protein and members of this family are coiled-coil proteins . Its primary role appears to be in ribosome biogenesis . Expression of CGR1 is also associated with a cessation of yeast cell growth, which is a prerequisite for germination in this organism .
DEAD box helicase DbpA/CsdA, RNA-binding domain (DbpA/CsdA_RNA-bd_dom)
Type: Domain

This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins .
Chromosome partition protein MukF (Chromosome_partition_MukF)
Type: Family

This family contains MukF, which are proteins involved in chromosome condensation, segregation and cell cycle progression. MukE along with MukF interact with MukB in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli . The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC . ScpA and ScpB have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly α-helical with coiled coil regions. The structure of MuKF has been revealed .
DNA-binding and peroxide stress resistance protein YaaA (YaaA)
Type: Family

YaaA (also refer to as DUF328/UPF0246) is involved in DNA recombination and oxidative stress response, being a key element of the stress response to H2O2. It acts by reducing the level of intracellular iron levels after peroxide stress, thereby attenuating the Fenton reaction and the DNA damage that this would cause . Yaa binds double-stranded, bulge-containing, bubble duplex and Holliday junction DNA with approximately equal affinity and ssDNA with lower affinity; DNA binding shows positive cooperativity . Structure analysis of this protein revealed a new fold with a positively charged cleft and a helix-hairpin-helix (HhH) DNA-binding motif named as cantaloupe fold.
DNA gyrase inhibitor YacG (DNA_gyrase_inhibitor_YacG)
Type: Family

This entry represents the DNA gyrase inhibitor YacG family.
E coli. YacG inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. It acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase . YacG has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins . The conserved four cysteine motif in this protein (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.
Protein of unknown function DUF327 (DUF327)
Type: Family

The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues, with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown.
ABC-type transport auxiliary lipoprotein component (ABC_trans_aux)
Type: Domain

This domain is found in a group of bacterial proteins that act as auxiliaries to the ABC-transporter in the gamma-hexachlorocyclohexane uptake permease system in Sphingobium japonicum. Gamma-hexachlorocyclohexane, or Lindane, can be used as the sole source of carbon in S.japonicum in aerobic conditions. Lindane is an insecticide .
Uncharacterised protein family UPF0304, YfbU (UPF0304_YfbU)
Type: Family

This is a family of functionally uncharacterised proteins with a length of about 160 residues. A member of this family, E. coli protein YfbU, has been structurally characterised and adopts an α-helical structure consisting of two subdomains. It forms a 24-subunit particle with an empty cavity. The N-terminal subdomains in this 24-mer pack around the 4-fold axis while the C-terminal domains interact at the 2-fold and 3-fold axes . In

this family is associated with a helix-turn-helix domain. This suggests that this may be a ligand-binding family.
MucB/RseB (MucB_RseB)
Type: Family

This entry includes sigma-E factor regulatory protein RseB and sigma factor AlgU regulatory protein MucB. RseB negatively modulates the activity of sigma-E (RpoE) by stabilizing RseA under non-stress conditions . MucB is a negative regulator of the sigma factor AlgU. It plays a role in the differentiation of P.aeruginosa into the alginate-producing form .
Alternative ribosome-rescue factor A (ArfA)
Type: Family

Alternative ribosome-rescue factor A (arfA) rescues ribosomes stalled at the 3' end of non-stop mRNAs . It binds the 30S subunit, contacting 16S rRNA with the N terminus near the decoding centre and its C terminus in the mRNA entry channel; contacts change in the presence of release factor 2 (RF2, also named PrfB) .
Protein of unknown function DUF333 (DUF333)
Type: Family

This family consists of functionally uncharacterised bacterial proteins.
Nitrate reductase cytochrome c-type subunit NapB (NapB)
Type: Family

The napB gene encodes a dihaem cytochrome c, the small subunit of a heterodimeric periplasmic nitrate reductase. The NapB protein is essential in transferring electrons to the large catalytic subunit NapA, which subsequently reduces nitrate to nitrite. .
Mono-/di-acylglycerol lipase, N-terminal (Mono/diacylglycerol_lipase_N)
Type: Domain

This N-terminal region is found in a family of mono-and diacylglycerol lipases.
Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase (Xul5P/Fru6P_PKetolase)
Type: Family

Phosphoketolases (PK) are key enzymes of the pentose phosphate pathway of heterofermentative and facultative homofermentative lactic acid bacteria and of the D-fructose 6-phosphate shunt of bifidobacteria. PK activity has been sporadically reported in other microorganisms including eukaryotic yeasts. Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase is a thiamine diphosphate (ThdP)-dependent enzyme found in bacteria such as Bifidobacterium sp . This enzyme has dual-specificity with the following catalytic activities:

: xylose 5-P + Pi = acetyl-P + glyeraldehyde-3-P

: fructose-6-P + Pi = acetyl-P + erythrose-4-P

Phosphoketolases are distantly related to transketolases, e.g.

.
Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain (YadA_C)
Type: Domain

The Yersinia adhesin A (YadA) is a trimeric autotransporter adhesin of enteric yersiniae. It consists of three major domains: a head mediating adherence to host cells, a stalk involved in serum resistance, and an anchor that forms a membrane pore and is responsible for the autotransport function .

This entry represents the C-terminal membrane anchor domain of YadA. Proteins containing this domain also include UspA2 from Moraxella , Eib immunoglobulin-binding proteins from E. coli, and DsrA proteins of Haemophilus ducreyi. These proteins are homologous at their C-terminal and have predicted signal sequences, but they diverge elsewhere. The C-terminal 9 amino acids, consisting of alternating hydrophobic amino acids ending in F or W, comprise a targeting motif for the outer membrane of the Gram-negative cell envelope. This region is important for oligomerisation .
Translocon-associated protein (TRAP), alpha subunit (TRAP_alpha)
Type: Family

The alpha-subunit of the TRAP (translocon-associated protein, also known as signal sequence receptor 1/alpha subunit, SSRA) complex is a single-spanning membrane protein of the endoplasmic reticulum (ER) . The four-subunit (alpha, beta, gamma and delta) TRAP complex localises in the ER membrane and associates with the Sec61 translocon as a heterotetramer . It also interacts with palmitoylated calnexin (CALX), the interaction is required for efficient folding of glycosylated proteins . TRAP complex may also be involved in endoplasmic reticulum-associated degradation . TRAP-alpha plays a critical role in the biosynthesis of insulin, being involved in preproinsulin translocation and proinsulin trafficking which may contribute to the pathogenesis of type 2 diabetes .
Satellite tobacco necrosis virus coat protein-like (Satellite_CP-like)
Type: Family

This entry represents the virus coat protein found in satellite tobacco necrosis virus, and maize white line mosaic Satellite virus. The protein contains a "jelly-roll" motif. The narrow end of the jelly roll is thought to form fivefold contacts organised about a Ca2+ ion .
ATP synthase protein I (ATP_synth_I)
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.

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 atp operon of most prokaryotes contains the structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein of unknown function. AtpI is thought to support optimal ATP synthase assembly and stability . A role in magnesium uptake has also been suggested .
GPI mannosyltransferase (GPI_mannosylTrfase)
Type: Family

Members of this family are glycosylphosphatidylinositol mannosyltransferase enzymes [ec:2.4.1.-] . At least some members are localised in endoplasmic reticulum and involved in glycosyl phosphatidyl inositol (GPI) anchor biosynthesis . In Arabidopsis, mannosyltransferase APTG1 (Abnormal Pollen Tube Guidance1) is required for pollen tube micropylar guidance and embryo development . In budding yeast, Smp3 (YOR149C) has been implemented in plasmid stability .
Gal4 dimerisation domain (Gal4_dimer_dom)
Type: Domain

The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of α-helix), is essential for dimerisation .
Tail fibre protein p36 (Tail_fibre_p36)
Type: Family

Irreversible binding of T-even bacteriophages to Escherichia coli is mediated by the short and long tail fibres, which serve as inextensible stays during DNA injection. Short tail fibres are exceptionally stable elongated trimers of gene product 12 (gp12), a 56kDa protein. The N-terminal region of gp12 is important for phage attachment, the central region forms a long shaft, while a C-terminal globular region is implicated in binding to the bacterial lipopolysaccharide core . Long tail fibers consist of a phage-proximal (gp34) and a phage-distal rod, the latter containing two protein trimers (gp36 and gp37). Gp36 is present in the upper part of the distal rod, it forms a complex with gp35 and gp37, binding them through the N-terminal and C-terminal regions, respectively. The upper part of the distal rod has a β-structure .
Protein of unknown function DUF334 (DUF334)
Type: Family

This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Coronavirus nonstructural protein NS4 (Corona_NS4)
Type: Family

This non-structural protein does not appear to be essential for viral growth in tissue culture and its physiological role is unknown.
Bacteriophage T7 tail fibre protein-like, N-terminal domain (Phage_T7_tail_fibre-like_N)
Type: Domain

The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17. The tail spike protein of bacteriophage K1F is important for the initial absorption of the phage into its host bacterium by hydrolysing the alpha-sialosyl linkages in the polysialic acid capsule . This entry represents the N-terminal domain of gp17 and similar phage proteins .
Sporulation-specific protein Spo7 (Spo7)
Type: Family

In budding yeasts, Spo7 is part of the Nem1-Spo7 protein phosphatase complex which acts as a phosphatase and dephosphorylates the phosphatidic acid phosphohydrolase PAH1 . The Nem1-Spo7 complex mediates regulation of membrane biogenesis is needed to promote mitophagy in yeast .
Sec20 (Sec20)
Type: Family

Sec20 is a membrane glycoprotein and a SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) involved in retrograde transport from the Golgi to the endoplasmic reticulum (ER) . It is also required for N- and O-glycosylation in the Golgi .
BSD domain (BSD_dom)
Type: Domain

The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see

) or the U-box in multidomain proteins. The function of the BSD domain is unknown .

Secondary structure prediction indicates the presence of three predicted α helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain .

Some proteins known to contain one or two BSD domains are listed below:

Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1).

Yeast RNA polymerase II transcription factor B 73kDa subunit (TFB1), the homologue of BTF2.

Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination.

Drosophila synapse-associated protein SAP47.

Mammalian SYAP1.

Arabidopsis thaliana (Mouse-ear cress) TFB1-1 (TFB1A) and TFB1-3 (TFB1C).
Adenovirus core-capsid bridging protein V (Adeno_V)
Type: Family

The Adenoviruses nucleoprotein core consists of genomic dsDNA and six proteins. Protein V is one of the most important proteins in the core due to its involvement in core condensation. Protein V also bridges the viral DNA core with the outer capsid by interacting with protein VI. It plays an important role in capsid assembly and in the formation of infectious virions .