SII-SWORD/CoKE huggingface dataset:
Trypanosome RHS (Trypano_RHS)
Type: Family

These sequences are full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position .
Large ribosomal subunit protein uL11, bacterial-type (Ribosomal_uL11_bac-typ)
Type: Family

Ribosomal protein uL11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, uL11
is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial, chloroplast, cyanelle, and most mitochondrial forms of ribosomal protein uL11. uL11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of uL11 has been shown to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure. This entry represents the bacterial, chloroplast and mitochondrial forms.

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 .
Distal tail protein, N-terminal (Dit_BPSPP_N)
Type: Domain

This entry represents the N-terminal domain of Distal tail protein (Dit) from Bacillus phage SPP1 (Bacteriophage SPP1) and similar proteins found in bacteriophages and temperate phage of mainly from Firmicutes. This domain is approximately 125 amino acids long.

Dit Forms a 40 Angstroms wide channel at the distal tip of the tail. It remains associated to the tail after DNA ejection .
Tail protein I (Tail_protein_I)
Type: Family

These sequences represent a family of phage tail proteins from phage P2 protein and related temperates phage of Gram-negative bacteria.
Phage virion morphogensis protein (Phage_virion_morphogenesis)
Type: Family

This entry represents a number of known and suspected phage virion morphogenesis proteins. The S protein from phage P2 is thought to act in tail completion and stable head joining .
Transcription activator RinA (RinA)
Type: Family

These sequences represent a family of phage (and phage-related) proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors .
Putative autolysin regulatory protein ArpU-like (ArpU-like)
Type: Family

This entry represents a group of proteins that includes Putative autolysin regulatory protein ArpU. ArpU was originally described as a regulator of cellular muramidase-2 of Enterococcus hirae , but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors, and it is proposed to be a phage transcriptional activator family. Members of this protein family are found in tailed bacteriophages (Caudovirales) and in Bacilli .
Cystatin-related, plant (Cystatin-related_pln)
Type: Domain

Sequences with this domain represent a family similar in sequence and probably homologous to a large family of cysteine proteinase inhibitors, or cystatins, as described by

. These proteins are only found in dicots. Cystatins may help plants resist attack by insects.
Exported protein, PHISTa/b/c, conserved domain, Plasmodium (Export_prot_PHISTa/b/c)
Type: Domain

This entry represents a conserved domain of about 60 amino acids that is found in several paralogues from Plasmodium falciparum, the apicomplexan parasite that causes the most severe form of malaria in humans. This domain is not currently found elsewhere, even in closely related Plasmodium species. Proteins that contain this domain include PHIST (for Plasmodium helical interspersed subtelomeric family) export proteins .
F-box associated domain, type 1 (F-box-assoc_dom_typ1)
Type: Domain

This domain occurs in a diverse superfamily of genes in plants. Most examples are found C-terminal to an F-box (

), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes . Some members have two copies of this domain.
Phage head morphogenesis domain (Phage_head_morphogenesis_dom)
Type: Domain

This domain is found in proteins found in the tailed bacteriophages Caudovirales and in bacterial prophages, internally or toward the C terminus.

Minor head protein GP7 from Bacillus phage SPP1 is required for viral head morphogenesis . Gp7 binds the viral DNA inside the capsid and the portal protein and may control the DNA exit from the virion .
U2 snRNP auxilliary factor, large subunit, splicing factor (U2AF_lg)
Type: Family

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs. The well-characterised members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (

). Members of this subfamily are found in plants, metazoa and fungi.
YD repeat (YD)
Type: Repeat

These sequences contain two tandem copies of a 21-residue extracellular repeat that is found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin .
Gp5/Type VI secretion system Vgr protein, OB-fold domain (Gp5/Vgr_OB)
Type: Domain

This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail . Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain.

It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells .

Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology .
Poly-U binding splicing factor, PUF60-like (PUF60-like)
Type: Family

Proteins in this family are DNA- and/or RNA-binding proteins involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation , containing three RNA recognition motifs . In the case of PUF60, in complex with p54, and in the presence of U2AF, it facilitates association of U2 snRNP with pre-mRNA . Poly(U)-binding-splicing factor rnp-6 from C.elegans is an homologue of mammalian PUF60 and it ensures the correct splicing of genes involved in immunity to promote longevity in response to infection by pathogenic bacteria such as S.aureus .
Type VI secretion system, RhsGE-associated Vgr protein (T6SS_Vgr_RhsGE)
Type: Family

This entry represent the Vgr family of proteins, associated with some classes of Rhs elements (Rhs classes G and E). Rhs (rearrangement hot-spot) elements are repetitious sequences identified in certain Escherichia coli strains .

Type VI secretion system (T6SS) appears to be confined to Proteobacteria. It is important for bacterial pathogenesis, but it is also found in non-pathogenic bacteria, suggesting that T6SS involvement is not limited to virulence . T6SS was identified in Vibrio cholerae and Pseudomonas aeruginosa , and exports Hcp (Haemolysin-Coregulated Protein) and a class of proteins named Vgr (Val-Gly Repeats). In addition to Vgr and Hcp proteins, T6SS is characterised by the presence of an AAA+ Clp-like ATPase and of two additional genes icmF and dotU, encoding homologues of T4SS stabilising proteins .
P-type ATPase, subfamily IIIA (P-type_ATPase_IIIA)
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.

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

This family represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds, and related bacterial and archaeal putative H(+)-ATPases. The best studied representative is from yeast .
HnRNP R/Q splicing factor (HnRNP_R/Q_splicing_fac)
Type: Family

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein) . These proteins contain three RNA recognition domains and a somewhat variable C-terminal domain.
HnRNP-L/PTB (HnRNP-L/PTB)
Type: Family

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L . These proteins contain four RNA recognition motifs.
Cobaltochelatase subunit CobS (PD_CobS)
Type: Family

These sequences are related to the Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit of MW ~37kDa that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in P. denitrificans) and an anaerobic pathway (found in Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation . There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction . Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobS in the aerobic pathway (P. denitrificans) is not a homologue of cobS in the anaerobic pathway (S. typhimurium). It should be noted that Escherichia coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their S. typhimurium homologues which function in the anaerobic cobalamin synthesis pathway . The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (

) and CobN (

CobN/magnesium chelatase) proteins.
Cobalt chelatase, CobT subunit (CobT)
Type: Family

These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised . Aerobic cobalt chelatase consists of three subunits, CobT, CobN (

) and CobS (

).

Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) . The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively . CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) .

Nomenclature note: CobT of the aerobic pathway P. denitrificans is not a homologue of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
P-type ATPase, subfamily IV (P-type_ATPase_IV)
Type: Family

This entry includes proteins members of the subfamily IV P-type ATPases. These ATPases are found in eukaryotes. Type IV ATPases have been shown to be involved in the transport of phospholipids , being involved in signal transduction, cell division, and vesicular transport.

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.
Bacteriocin, lactococcin 972 (Lactococcin_972)
Type: Family

These sequences represent bacteriocins related to lactococcin 972 . Members tend to be found in association with a seven transmembrane putative immunity protein.
Bacteriocin-associated integral membrane protein (Bacteriocin_ass)
Type: Family

These sequences represent a family of integral membrane proteins, most of which are about 650 residues in size and predicted to span the membrane seven times. Nearly half of the members of this family are found in association with a member of the lactococcin 972 family of bacteriocins (

) . Others may be associated with uncharacterised proteins that may also act as bacteriocins. Although this protein is suggested to be an immunity protein, and the bacteriocin is suggested to be exported by a Sec-dependent process, the role of this protein is unclear.
Protein of unknown function DUF1093 (DUF1093)
Type: Family

These are a family of small (about 115 amino acids) uncharacterised proteins with N-terminal signal sequences, found predominantly in Gram-positive organisms. Most genomes that have any members of this family have at least two members. This entry includes YxeA from Bacillus subtilis, which gene is located in operon encoding the ABC transporter structural genes YxdJKLM. YxeA is transcriptionally regulated by YxdJ . It is predicted to participate in antibiotic resistance mechanism as an immunity peptide interacting with and neutralising antibiotic.
Histidinol-phosphate phosphatase (Histidinol-phos)
Type: Domain

This is a group of authentic histidinol-phosphate phosphatases which are sometimes found as stand-alone entities and sometimes as fusions with imidazoleglycerol-phosphate dehydratase. Additionally, a family of proteins including YaeD from Escherichia coli and various other proteins are closely related but may not have the same substrate specificity. This protein is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing a conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the region modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3.
P-type ATPase, subfamily V (P-type_TPase_V)
Type: Family

This entry includes P-type ATPases from eukaryotes that form a different clade, designated subfamily V (P5-ATPases) . P-type ATPases use ATP for intracellular cation homeostasis and are required for proper lysosomal and mitochondria maintenance , also playing a role in the maintenance of neuronal integrity . P5-type ATPases can be subdivided in two subtypes based on the conservation of residues in the transmembrane domain, the P5A-type, which localize to the ER membrane (ATP13A1 from human and SPF1 from yeast), and P5B-type ATPases which are vacuolar or lysosomal membrane-associated proteins. Humans express four isoforms, ATP13A2 to ATP13A5 .

SPF1 from yeast and ATP13A1 are ER translocases required to remove mitochondrial transmembrane proteins mistargeted to the endoplasmic reticulum . They were initially thought to mediate ion transport such as calcium or manganese but then it was reported that they specifically binds moderately hydrophobic transmembrane with short hydrophilic lumenal domains that misinsert into the endoplasmic reticulum .

Human ATP13A2 (also known as PARK9), the most studied member of the P5B-type, is a neuroprotective ATPase enriched in the brain that selectively imports spermine ions from lysosomes into the cytosol . Mutations ATP13A2 cause a rare monogenic form of juvenile-onset Parkinson's disease named Kufor-Rakeb syndrome and other neurodegenerative diseases .

This entry includes also other isoforms such as ATP13A3, ATP13A4, ATP13A5.

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

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.
EYA domain (EYA_dom)
Type: Domain

The Eyes absent proteins are members of a conserved regulatory network implicated in the development of the eye, muscle, kidney and ear. Eyes absent is a nuclear transcription factor, acting through interaction with homeodomain-containing Sine oculis (also known as Six) proteins. Eyes absent is also a protein tyrosine phosphatase , It does not resemble the classical tyrosine phosphatases that use cysteine as a nucleophile and proceed by means of a thiol-phosphate intermediate. Rather, Eyes absent is the prototype for a class of protein tyrosine phosphatases that use a nucleophilic aspartic acid in a metal-dependent reaction. Furthermore, the phosphatase activity of Eyes absent contributes to its ability to induce eye formation in drosophila. Thus, Eyes absent belongs to the phosphatase subgroup of the haloacid dehalogenase (HAD) superfamily and appears to act as a nuclear transcriptional coactivator with intrinsic phosphatase activity.

The Eyes absent proteins contain a divergent 200-300 residue long N-terminal region and a conserved C-terminal domain of approximately 270 residues, the EYA domain, which is critical for activity and believed to participate in protein-protein interactions .
Sex-lethal splicing factor (Sxl)
Type: Family

These sequences describe the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species . In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (

).

SXL (sex-lethal) governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster . It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing . SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs) that show high preference to bind single-stranded, uridine-rich target RNA transcripts .