SII-SWORD/CoKE huggingface dataset:
Pseudouridine synthase TruD, conserved site (PsdUridine_synth_TruD_CS)
Type: Conserved_site

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are :

Pseudouridine synthase I, TruA.

Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.

Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.

Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.

Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.

Pseudouridine synthase TruD modifies uracil-13 in tRNA . TruD belongs to a large family of pseudouridine synthases present in all kingdoms of life . It folds into a V-shaped molecule with an RNA-binding cleft formed between its two domains: a catalytic domain and an insertion domain. The catalytic domain differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases. The insertion (or TRUD) domain displays an α/β structure that forms a compact fold titled away from the catalytic domain to create a deep cleft in TruD which is lined with basic residues from each domain. The insertion domain is characterised by two conserved sequence motifs that form a part of the hydrophobic core, as well as by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologues. The insertion domain is likely to be involved in substrate recognition and may represent a RNA binding module .
Plasmid pGKL2, Orf8 (Plasmid_pGKL2_Orf8)
Type: Family

The proteins in this entry represent Orf8 from killer plasmid K2 (pGKL2) of Kluyveromyces lactis (Yeast) (Candida sphaerica). K2 contains ten open reading frames. Some of the ORFs overlap on different strands and some on the same strand and at least 8 of the 10 ORFs are transcribed. Comparison of the sequence of pGKL2 to the sequence of the K2 plasmid from Saccharomyces cerevisiae strain F102-2 revealed only one nucleotide difference showing a very high degree of conservation of the plasmid sequences from the two yeasts .
Bacteriophage T7-like gene 6.5 (Phage_T7-like_6.5)
Type: Family

The proteins in this entry are uncharacterised.
Alphabaculovirus, Y056 (Alphabaculovirus_Y056)
Type: Family

This protein family contains uncharacterised proteins mainly found in Alphabaculovirus, including Uncharacterized 9.7 kDa protein from Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) and Uncharacterized 9.9 kDa protein in LEF8-FP intergenic region from Autographa californica nuclear polyhedrosis virus (AcMNPV).
Protein of unknown function DUF5475 (DUF5475)
Type: Family

This is a family of unknown function found in Alphabaculovirus.
Protein of unknown function DUF5488 (DUF5488)
Type: Family

This is a family of unknown function found in Orthopoxvirus.
Protein of unknown function DUF2732 (DUF2732)
Type: Family

This entry represents a group of proteins with no known functio
Colicin-E5 immunity protein (Colicin-E5_imm)
Type: Family

Colicins, which are produced by bacteria carrying the corresponding Col plasmids, kill sensitive Escherichia coli cells using different mechanisms. Colicin E5 is a tRNase toxin. The immunity protein ImmE5 is a specific inhibitor of colicin E5 that is expressed to protect the host cells. It binds to E5 C-terminal ribonuclease domain (CRD) to prevent cell death .
Secapin (Secapin)
Type: Family

This entry represents Secapin; a nontoxic peptide found in the venom of bees and wasps, a serine protease inhibitor which exhibits antifibrinolytic, antielastolytic and antimicrobial activities against bacteria and fungi . It may function in the innate immune response to microbial infection and possibly in the venom, as an antifibrinolytic agent . Secapin shares a common folding pattern with apamin, mast cell degranulating peptide and tertiapin; it is centred on a β-turn covalently linked to an α-helical segment by one disulphide link (two disulphide links in the other peptides) . Secapin-2 induces hyperalgesia and edema mediated by leukotrienes when injected into mice and it does not induce hemolytic activity, mast cell degranulation, or chemotactic activity for polymorphonucleated leukocytes (PMNL) .
Spanin, outer lipoprotein subunit, T7likevirus (O-spanin_T7likevirus)
Type: Family

The lysis of Gram-negative hosts by double-strand DNA bacteriophages requires, in addition to the actions of a holin and endolysin, a third step involving the spanin complex. This complex consists of a small outer membrane lipoprotein and an integral cytoplasmic membrane protein, designated as o-spanins and i-spanins, respectively. The spanin complex is involved in the disruption of the outer membrane. Without the spanin function, lysis is blocked and progeny virions are trapped in dead spherical cells .

This entry represents the o-spanin subunit from T7likevirus.
Mycobacteriophage tail assembly protein 24/25 (Gp24/Gp25)
Type: Family

This entry includes the tail assembly protein Gp24 and Gp25. In some strains Gp24 is the N-terminal domain of a fusion protein with the following ORF, Gp25. In Mycobacteriophages these proteins are likely to interact with the tape measure protein .
Decidual protein, progesterone induced (DEPP)
Type: Family

This entry represents proteins from various mammals known as DEPP proteins, which are decidual proteins induced by progesterone.

Decidualization of the endometrial stromal cells (ESC) is thought to be stimulated by progesterone and/or cAMP and is crucial for embryo implantation and placentation. Increased expression of Depp was observed in endometria during mid- and late-secretory phases and 1st trimester deciduas. Depp increased the level of phosphorylated Erk and activated the Elk-1 transcription factor in human embryonal kidney 293 cells, suggesting that Depp modulates the effects of progesterone during decidualization and in the decidua by affecting gene expression .
Bacteriophage T7-like, protein 6.7 (Phage_T7-like_6.7)
Type: Family

Protein 6.7 is ejected from the infecting virion. It is found in tail-less particles and has been defined as a head protein .
Uncharacterised protein family RP854 (Uncharacterised_RP854)
Type: Family

This entry represents proteins related to RP854 from Rickettsia prowazekii. They are currently uncharacterised.
Uncharacterised protein family YqzF (Uncharacterised_YqzF)
Type: Family

This entry represents uncharacterised membrane proteins with no known function.
Protein of unknown function DUF2642 (DUF2642)
Type: Family

This entry contains proteins with no known function.
Uncharacterised protein family YusG (Uncharacterised_YusG)
Type: Family

This entry contains proteins with no known function.
Herpesvirus UL41A (Herpesvirus_UL41A)
Type: Family

This entry represents proteins from Herpesvirus. The protein UL41A is thought to be a membrane associated glycoprotein but is currently uncharacterised.
Protein of unknown function DUF5489 (DUF5489)
Type: Family

This is a family of unknown function found in Alphafusellovirus.
Stage V sporulation protein AB (SpoVAB)
Type: Family

This entry represents stage V sporulation protein AB (SpoVAB), which is involved in spore germination and is located in the spores' inner membrane. In Bacillus subtilis, SpoVA proteins are a component of a dipicolinic acid (DPA) channel in the spore's inner membrane and are involved in DPA release .
Inhibitor of dGTPase, bacteriophage T7-like (Phage_T7-like_1.2)
Type: Family

The T7-like bacteriophage gene 1.2 protein is an inhibitor of the Escherichia coli dGTP triphosphohydrolase (dGTPase) and is implicated in DNA replication.
Protein of unknown function DUF5477 (DUF5477)
Type: Family

This is a family of proteins of unknown function found in phages.
Uncharacterised protein family C02F5.10 (Uncharacterised_C02F5.10)
Type: Family

The proteins in this entry are uncharacterised.
Type IV conjugative transfer system protein TrbE (T4SS_TrbE)
Type: Family

TrbE is encoded by the F-plasmid and is located between traN and traF. The product of trbE is a small, integral, inner membrane protein. Mutation of trbE by insertional mutagenesis suggests that TrbE is not essential for F transfer from Escherichia coli (strain K12) under standard mating conditions .
Protein of unknown function DUF5478 (DUF5478)
Type: Family

This is a family of unknown function found in Alphabaculovirus.
Uncharacterised protein family YeiS (Uncharacterised_YeiS)
Type: Family

This entry represents transmembrane proteins with no known function.
Protein of unknown function DUF5490 (DUF5490)
Type: Family

This is a family of unknown function found mainly in Myoviridae.
Uncharacterised protein family YqkC (Uncharacterised_YqkC)
Type: Family

This entry contains proteins with no known function.
Protein of unknown function DUF2756 (DUF2756)
Type: Family

This entry contains proteins with no known function.
Phage Tail fiber assembly helper gene product 57 (Phage_Gp57)
Type: Family

Gene product 57 (Gp57) is a chaperone protein for short tail fibre phage protein, that acts as a molecular chaperone of gp12, increasing the folding efficacy and production efficiency .
Cell cycle exit/neuronal differentiation protein 1 (Cend1)
Type: Family

Cell cycle exit and neuronal differentiation protein 1 (Cend1 or BM88) is a homodimer of 140 amino acids. It has a putative transmembrane domain at the C terminus. The mRNA of this protein is expressed only in neural tissues, where it is restricted to neurons. It is involved in neuroblastoma cell differentiation , neuronal differentiation , and development of the cerebellum .
Cytochrome c oxidase assembly protein COX16 (Cyt_c_Oxase_assmbl_COX16)
Type: Family

Cytochrome c oxidase assembly protein COX16 is required for the assembly of cytochrome c oxidase . It is found in the inner membrane of the mitochondrion.
Uncharacterised protein family RP363/RP364 (Uncharacterised_RP363/RP364)
Type: Family

This entry represents proteins that are confined to Rickettsiales. The proteins include RP363 and RP364, which are currently uncharacterised.
Intrinsic membrane protein family, PufX (Intrinsic_membrane_PufX)
Type: Family

PufX organises RC-LH1, the photosynthesis reaction centre-light harvesting complex 1 core complex of Rhodobacter sphaeroides . It also facilitates the exchange of quinol for quinone between the reaction centre and cytochrome bc(1) complexes. In organic solvent, PufX contains two hydrophobic helices which are flanked by unstructured regions and connected by a helical bend .
Herpesvirus UL11, muromegalovirus/roseolovirus-type (Herpes_UL11_megaloV/roseoloV)
Type: Family

UL11 (also known as cytoplasmic envelopment protein 3) is conserved throughout the herpesvirus family. It is a membrane-associated tegument protein that is incorporated into the HSV virion. UL11 and UL51, either singly or in combination, are involved in virion envelopment and/or egress. Both proteins are fatty acylated. UL11 is acylated by both myristoic and palmitoic acids while UL51 is mono-acylated by palmitoic acid . UL11 homologue (U71) from HHV-6A/B is a myristylated virion protein which is expressed at the early stage of the lytic cycle . Proteins in this entry are from the muromegalovirus and roseolovirus groups.
Uncharacterised protein family RC0039 (Uncharacterised_RC0039)
Type: Family

This entry represents proteins that are confined to Rickettsiales. The proteins, which include RC0039 and RP030, are currently uncharacterised.
Herpesvirus glycoprotein L, rhadinovirus-type (Herpes_gL_rhadinovirus)
Type: Family

Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen .

Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH .
Uncharacterised protein family RP853 (Uncharacterised_RP853)
Type: Family

This entry represents proteins that are confined to Rickettsia. The family member RP853 is thought to be a transmembrane protein, but is currently uncharacterised.
Ant venom allergen, Sol i 2 (Ant_venom_allergen_Sol_i_2)
Type: Family

Fire ant venom from Solenopsis invicta (Red imported fire ant), is an extremely potent allergy-inducing agent containing four major allergens, Sol i 1 to Sol i 4 .

This family contains the allergens Sol i 2. Sol i 2 causes IgE antibody production in about one-third of individuals stung by fire ants. This allergen is a disulphide-linked homodimer .
Protein of unknown function DUF5460 (DUF5460)
Type: Family

This is a family of unknown function found in Rickettsia. Family members are predicted to contain one trans-membrane region.
Uncharacterised protein family RC0048 (Uncharacterised_RC0048)
Type: Family

This entry represents proteins that are mainly confined to Rickettsia and Orientia. The proteins, which include RP364 and RC0048, are currently uncharacterised.
Keratin-associated protein 7 (KRTAP7)
Type: Family

This family includes keratin-associated protein 7-1, a member of the type 7 family. In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulphide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulphur and high-glycine-tyrosine keratins.

Other groups of keratin-associated proteins include

and

.
Spore morphogenesis/germination protein YwcE (Spore_morphogenesis_YwcE)
Type: Family

Spore morphogenesis and germination protein YwcE is required for proper spore morphogenesis and germination. It is repressed by abrB during growth and activated at the onset of sporulation in a spo0A-dependent manner. This protein has similar features to holin .
Meiosis-expressed gene 1 protein (Meiosis-expressed_gene_1)
Type: Family

This entry represents Meiosis-expressed gene 1 protein and its homologues, encoded by the gene MEIG1. It may be involved in germ cell differentiation during meiotic prophase. Sequence analysis predicts this protein to be 10.8kDa in size and to be highly charged and lysine rich .
Translation elongation factor, IF5A C-terminal (Transl_elong_IF5A_C)
Type: Domain

A five-stranded β-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded β-sheet coiled to form a closed β-barrel capped by an α helix located between the third and fourth strands . Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case .

There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 .

This entry represents the RNA-binding domain of translation elongation factor IF5A .
Procorazonin (Procorazonin)
Type: Family

In Drosophila melanogaster (Fruit fly) the preprocorazonin consists of an 19 amino acid signal peptide, the 11 amino acid corazonin sequence followed by a 39 amino acid corazonin-precursor-related peptide (CPRP) and finally the 85 amino acid propeptide,

.

Corazonin is a cardioactive peptide of insects, which is probably involved in the physiological regulation of the heart beat. Drosophila clock (clk) and cycle (cyc) proteins negatively regulate Crz transcription in a cell-specific manner . Corazonin is expressed in neurosecretory neurons of the pars lateralis of the protocerebrum and transported via nervi corporis cardiaci to the storage lobes of the corpora cardiaca. The peptide occurs with a single isoform in all insects studied so far, with the exception of the Coleoptera in which none could be detected .
SWR1 chromatin-remodelling complex, subunit Swc7 (SWR1_Swc7)
Type: Family

This entry represents the subunit Swc7; the smallest subunit of the SWR1 complex. Swc7 is not required for H2AZ binding. Swc7 associates with the N terminus of Swr1, and the association of Bdf1 requires Swc7, Yaf9, and Arp4 .

The SWR1 complex is involved in chromatin-remodelling by promoting the the ATP-dependent exchange of histone H2A for the H2A variant HZT1 in Saccharomyces cerevisiae (Baker's yeast) or H2AZ in mammals. The SWR1 chromatin-remodelling complex is composed of at least 14 subunits and has a molecular mass of about 1.2 to 1.5 MDa. In S. cerevisiae the core conserved subunits are:

ATPase; Swr1.

RuvB-like; Rvb1 and Rvb2.

Actin; Act1.

Actin-related: Arp4 and Arp6.

YEATS protein ; Yaf9.

The non-conserved subunits are: Vps71 (Swc6), Vps72 (Swc2), Swc3, Swc4, Swc5, Swc7, Bdf1 .

Seven of the SWR1 subunits are involved in maintaining complex integrity and H2AZ histone replacement activity: Swr1, Swc2, Swc3, Arp6, Swc5, Yaf9 and Swc6. Arp4 is required for the association of Bdf1, Yaf9, and Swc4 and Arp4 is also required for SWR1 H2AZ histone replacement activity in vitro. Furthermore the N-terminal region of the ATPase Swr1 provides the platform upon which Bdf1, Swc7, Arp4, Act1, Yaf9 and Swc4 associate ; it also contains an additional H2AZ-H2B specific binding site, distinct from the binding site of the Swc2 subunit .
Uncharacterised protein family YqgB (Uncharacterised_YqgB)
Type: Family

The yqgB and yqfZ genes are associated with the genomes of bacteria with distinct pathogenic properties and consequently fall into the category of being virulence genes . However, yqgB and yqfZ genes are not true virulence factors but instead are probably lifestyle determinant genes where the gene products act in concert, enabling the bacteria to cope with its suboptimal physical environment and thus facilitating host colonization .
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52 (AcMNPV_Orf52)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Atracotoxin (Atracotoxin)
Type: Family

This entry represents various Atracotoxin proteins that are secreted from Hexathelidae (funnel-web tarantulas). They are thought not to be toxic to insects or mammals, having no effect on smooth muscle contractility .
Membrane protein YneK (YneK)
Type: Family

This is a group of uncharacterised membrane bacterial proteins.
Uncharacterised protein family, YxaJ (Uncharacterised_YxaJ)
Type: Family

This entry represents a group of uncharacterised transmembrane proteins.
Uncharacterised protein family, YwnF, transmembrane (Uncharacterised_YwnF_TM)
Type: Family

This entry represents a group of uncharacterised transmembrane proteins.
Uncharacterised protein family, VP2110 (Uncharacterised_VP2110)
Type: Family

This entry represents a group of uncharacterised proteins.
Metastasis-suppressor KiSS-1 (Metastasis-suppressor_KiSS-1)
Type: Family

Kisspeptin (KiSS-1) is a metastasis suppressor protein found in malignant melanomas and in some breast cancers . KiSS-1 may regulate events downstream of cell-matrix adhesion, which could involve cytoskeletal reorganisation. KiSS-1 generates a C-terminally amidated peptide, metastin, which functions as the endogenous ligand of the G-protein coupled receptor GPR54. Activation of the receptor inhibits cell proliferation and cell migration, key characteristics of tumour metastasis. Kp-10 is a decapeptide derived from the primary translation product, isolated in conditioned medium of first trimester trophoblast . Kp-10, but not other kisspeptins, increased intracellular Ca2+ levels in isolated first trimester trophoblasts. Kp-10 is a paracrine/endocrine regulator in fine-tuning trophoblast invasion generated by the trophoblast itself. The receptor is also essential for normal gonadotropin-released hormone physiology and for puberty. The hypothalamic KiSS1/GPR54 system is a pivotal factor in central regulation of the gonadotropic axis at puberty and in adulthood .
Protein of unknown function DUF2712 (DUF2712)
Type: Family

This entry represents a group of uncharacterised proteins.
Cas6b, C-terminal domain (Cas6b_C)
Type: Domain

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation . Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense .
Uncharacterised protein family, YpbF, transmembrane (Uncharacterised_YpbF_TM)
Type: Family

This entry represents a group of uncharacterised transmembrane proteins.
Toxin coregulated pilus biosynthesis protein TcpS (Toxin-coreg_pilus_synth_TcpS)
Type: Family

Toxin coregulated pilus biosynthesis protein S (TcpS) is part of an operon associated with biosynthesis of the toxin coregulated pilus (TCP) of Vibrio cholerae . TCP is essential for successful colonisation of the bacteria in the small intestine. The genes tcpR, tcpD, tcpS, tcpT, tcpE and tcpF are organised to permit translational coupling and are followed by an inverted repeat structure which is likely to act as a strong Rho-independent terminator . TcpS possesses an N-terminal signal sequence, suggesting that it is localised to the periplasm.
Cytomegalovirus UL124 (Cytomega_UL124)
Type: Family

This is a family of unknown function found in cytomegalovirus. Family member UL124 is a predicted membrane glycoprotein with one predicted trans-membrane region .
EbsA-like (EbsA-like)
Type: Family

The pore-forming protein EbsA is one of three proteins (EbsA, EbsB, and EbsC) that affects the expression of a chromosomally encoded receptor, named binding substance (BS). In Enterococcus faecalis (Streptococcus faecalis), transfer of the conjugative plasmid pCF10 involves production of a plasmid-encoded aggregation substance in response to stimulation by a pheromone secreted by recipient cells . The aggregation substance then facilitates attachment to recipient cells via the BS receptor. Both ebsA and ebsB encode peptides likely to function in cell wall metabolism, where EbsA may assist in the localisation of EbsB to the cell wall. EbsC may encode a product that suppresses the function or expression of EbsB .
Uncharacterised protein family, YncE (Uncharacterised_YncE)
Type: Family

This entry represents a group of uncharacterised proteins.