SII-SWORD/CoKE huggingface dataset:
Herpesvirus U10 (Herpes_U10)
Type: Family

This proteins in this entry belong to the herpesvirus U10 family.

Family member Protein UL31 is involved in the inhibition of the host innate immune system. It targets host CGAS, promoting dissociation of DNA from CGAS, thus inhibiting the enzymatic activity of CGAS .
Poxvirus T4 protein, C-terminal (Poxvirus_T4p_C)
Type: Domain

This entry represents the C-terminal domain of T4 protein from Sheeppox virus, Protein OPG195 from Monkeypox virus, and similar sequences from poxvirus. T4 is thought to be retained in the endoplasmic reticulum. M-T4 of myxoma virus (

) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection . CPXV203 protein from Cowpox virus (

) binds a wide array of proteins from the major histocompatibility complex class I (MHCI) in a pH dependent manner . The N terminus is represented by

.
Poxvirus T4 protein, N-terminal (Poxvirus_T4p_N)
Type: Domain

This entry represents the N-terminal domain of T4 protein from Sheeppox virus, Protein OPG195 from Monkeypox virus, and similar sequences from poxvirus. T4 protein is thought to be secreted or retained in the endoplasmic reticulum if the protein also contains an additional C-terminal region (

). M-T4 of myxoma virus (

) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection . CPXV203 protein from Cowpox virus (

) binds a wide array of proteins from the major histocompatibility complex class I (MHCI) in a pH dependent manner .
Endonuclease V (Endonuclease-V)
Type: Family

Endonuclease V is specific for single-stranded DNA, for duplex DNA that contains uracil, or that is damaged . Matrix metalloproteinase-1 (MMP-1) is the major enzyme responsible for collagen 1 digestion. It is induced by exposure to sunlight, but is reduced with treatment of DNA repair enzyme endonuclease V . This family consequently has potential medical importance .

This endonuclease also appears in bifunctional enzymes, such as the bifunctional methyltransferase/endonuclease in Thermoplasma acidophilum.
TFIID subunit TAF5, NTD2 domain (TFIID_NTD2)
Type: Domain

This region is an all-alpha domain associated with the WD40 helical bundle of the TAF5 subunit of transcription factor TFIID. The domain has distant structural similarity to RNA polymerase II CTD interacting factors. It contains several conserved clefts that are likely to be critical for TFIID complex assembly . The TAF5 subunit is present twice in the TFIID complex and is critical for the function and assembly of the complex, and the NTD2 (second N-terminal domain) and N-terminal domain are crucial for homodimerisation . TAF5 has a paralogue gene (TAF5L) which has a redundant function .

The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID .
GRASP55/65 (GRASP55_65)
Type: Family

GRASP55 (Golgi reassembly stacking protein of 55kDa) and GRASP65 (a 65kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65 is an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system .
Herpesvirus UL35 (Herpes_UL35)
Type: Family

The small capsomere-interacting protein (SCP, also known as UL35 or VP26) represents a true late gene which encodes a 12kDa capsid protein . SCP forms a complex with the major capsid protein in the cytoplasm which is translocated to the nucleus. SCP decorates the outer surface of the capsid shell during capsid assembly, forming a layer between the capsid and the tegument. The interaction between SCP with host dynein light chains is a possible mechanism for the transportation of incoming viral capsids .
Poxvirus E2 (Poxvirus_E2)
Type: Family

This entry represents Protein E2 from Vaccinia virus, also known as Protein OPG064, and similar sequences from poxvirus. E2 plays a role in intracellular enveloped virus (IEV) transport to the cell surface on microtubules. Together with protein OPG056/F12, it forms a complex that interacts with host KLC2 (kinesin light chain isoform 2) to engage the kinesin-1 complex and thereby promote IEV traffic . E2 shows two domains: an N-terminal annular (ring) domain and a C-terminal globular (head) domain .
Poxvirus VP8/L4R, nucleic acid binding (VP8_pox_nuc-bd)
Type: Family

The 25kDa product of Vaccinia virus gene L4R is also known as VP8. VP8 is found in the cores of Vaccinia virions and is essential for the formation of transcriptionally competent viral particles. It binds both single stranded and double stranded DNA and RNA with similar affinities. Binding is thought to involve cooperative interactions between protein subunits. The protein is proteolytically cleaved during viral assembly at an Ala-Gly-Ala site. Possible roles for VP8 include packaging and maintaining the DNA genome in a transcribable configuration; binding ssDNA during transcription initiation; and cooperation with I8R protein to unwind early promoter regions. VP8 may also function in either transcription elongation or release of mRNA molecules from viral particles .
SIT4 phosphatase-associated protein family (SAPS)
Type: Family

This entry includes budding yeast Sit4-associated proteins, such as Sap155, Sap185, and Sap190. Sit4 is a phosphatase involved in a variety of processes including transcription, translation, bud formation, glycogen metabolism, monovalent ion homeostasis, H+ transport, and telomere function .

This entry also includes mammalian PP6 (Sit4 homologue)-associated proteins, such as PP6R1, PP6R2, and PP6R3 . They are regulatory subunits of PP6 involved in the PP6-mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF-alpha .
Baculovirus major capsid protein VP39 (Baculo_VP39)
Type: Family

This family constitutes the 39kDa major capsid protein of the Baculoviridae .
Saf4/Yju2 protein (Saf4/Yju2)
Type: Family

This entry includes Probable splicing factor YJU2B (also known as CCDC130) and Splicing factor YJU2 (also known as CCDC94) from humans, Saf4 from fission yeasts and Yju2 from budding yeasts. Saf4 (also known as cwc16) is involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome . Yju2 is a splicing factor that is associated with the Prp19-associated complex and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing. It may play a role in stabilizing the structure of the spliceosome catalytic core .
GLABROUS1 enhancer-binding protein-like (GEBP)
Type: Family

This family of plant transcription factors includes GLABROUS1 enhancer-binding protein (GeBP) and GeBP-like proteins, and storekeeper and storekeeper-like (STKL) transcription factors.

GeBP and GeBP-like proteins play a redundant role in cytokinin hormone pathway regulation . Storekeeper was identified as a B-box motif binding factor that regulates expression of patatin, a storage protein in potato . Storekeeper-like transcription factors STKL1 and STKL2 function as transcription factors in the glucose signaling pathway .
CD225/Dispanin family (CD225/Dispanin_fam)
Type: Family

This family represents a set of transmembrane proteins including various interferon-induced transmembrane proteins, synapse differentiation-inducing gene protein 1, and tumor suppressor candidate 5 and homologues. Interferon-induced transmembrane protein 1 (also known as human leukocyte antigen CD225) regulates vesicular membrane fusion events and is essential for different physiological processes such as interferon induced cell growth suppression, neurotransmision and metabolism .
RFT1 (RFT1)
Type: Family

This entry represents the Man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1, and related proteins, requited for the translocation of lipid-linked oligosaccharides across the ER membrane . Rft1 may have a critical accessory role in translocating Man(5)GlcNAc(2)-PP-Dol in vivo .

Asymmetric lipid distribution is a fundamental characteristic of biological lipid bilayers, one such axample is the translocation of the Man
5
GlcNAc
2
-PP-Dol intermediate from the cytosolic side of the ER membrane to the lumen before the completion of the biosynthesis of Glc
3
Man
9
GlcNAc
2
-PP-Dol . RFT1 encodes an evolutionarily conserved protein required for this translocation.
Csa family (Csa)
Type: Family

This family contains several uncharacterised proteins mostly from staphylococcal. These proteins have been called conserved staphylococcal antigens (Csa) .
Viral A-type inclusion protein repeat (Pox_A_type_inc)
Type: Repeat

The repeat is found in the A-type inclusion protein of the Poxvirus family .
CheC-like protein (CheC)
Type: Domain

The precise function of these proteins is unclear, but some of them are involved in flagella motor switch . The region represented in this entry is found in the CheC, CheX, CheA and FliY proteins. In some cases, this region is repeated in multiple copies.
Domain of unknown function DUF577 (DUF577)
Type: Domain

This domain is found in Arabidopsis thaliana (Mouse-ear cress) putative proteins which are specifically expressed during meiosis . Many of these members contain a repeated region.
Derlin (DER1)
Type: Family

The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae (Baker's yeast) contains a proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process, and the classes were called der for degradation in the ER. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins, suggesting that the function of the Der1 protein may be specifically required for the degradation process associated with the ER . Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. This family may also mediate degradation of misfolded proteins.
Baculovirus polyhedron envelope protein PEP, N-terminal (Baculo_PEP_N)
Type: Domain

Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilise polyhedra and protect them from fusion or aggregation .
Baculovirus polyhedron envelope protein PEP, C-terminal (Baculo_PEP_C)
Type: Domain

Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilise polyhedra and protect them from fusion or aggregation .
Bluetongue virus nonstructural protein NS2 (BTV_NS2)
Type: Family

This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA-binding regions have been identified in Bluetongue virus 17 (

) at residues 2-11, 153-166 and 274-286 . NS2 multimers also possess nucleotidyl phosphatase activity . The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs .
Choline transporter-like (Choline_transptr-like)
Type: Family

This entry includes a group of choline transporter-like protein, including SLC44A1/2/3/4/5 from humans, Pns1 from budding yeasts, and Ctl1 from fission yeasts . In humans, mutations of this family of proteins have been linked to several human diseases .
CP2 transcription factor (CP2)
Type: Domain

This entry represents a domain found in animal and fungal Grh/CP2 transcription factors (TFs), key regulators of epithelial differentiation, organ development and skin barrier formation. The Grh/CP2 family of TFs comprises two distinct divisions, CP2 (CCAAT box-binding protein 2) and Grh (grainyhead). Proteins of the CP2 subfamily are generally expressed ubiquitously, while the expression pattern of the Grh subfamily is rather tissue- and developmental stage specific. All Grh/CP2 family members share a common domain architecture characterised by an intrinsically unstructured N-terminal transactivation domain (TAD), a conserved DNA-binding domain (DB, also termed CP2 binding domain), and a C-terminal dimerisation domain (DD). The Grh/CP2 DB domain contains an immunoglobulin (Ig)-like core with two long, twisted antiparallel β sheets of five and six strands, respectively. This core is decorated by three α helices and a series of surface loops .
Microvirus lysis protein (E) (Micrvir_lysisE)
Type: Family

E protein causes host cell lysis by inhibiting MraY, a peptidoglycan biosynthesis enzyme. This leads to cell wall failure at septation . The N-terminal transmembrane region matches the signal peptide model and must be omitted from the family.
Type III secretion system effector (T3SS_effector)
Type: Family

This is a family of Chlamydial effector proteins which are secreted by the type III secretion system . The precise function of this family is unknown.
Bactofilin A/B (BacA/B)
Type: Family

This is a family of bactofilins, a functionally diverse class of cytoskeletal, polymer-forming, proteins that is widely conserved among bacteria, such as BacP, BacN and BacO from Myxococcus xanthus, which are non-essential components of the chromosome segregation machinery .
These proteins position the ParA-ParB-parS chromosome segregation machinery within the cell; BacP seems to be the most important bactofilin in this process . They form a heteropolymeric, subpolar scaffold in the cell in which BacP probably forms the core, BacO contributes to position and integrity while BacN does not seem to contribute to assembly . In C. crescentus, two bactofilins assemble into a membrane-associated laminar structure that shows cell-cycle-dependent polar localisation and acts as a platform for the recruitment of a cell wall biosynthetic enzyme involved in polar morphogenesis. Bactofilins display distinct subcellular distributions and dynamics in different bacterial species, suggesting that they are versatile structural elements that have adopted a range of different cellular functions .
Senescence regulator S40 (Senescence_reg_S40)
Type: Family

Proteins in this family include AtS40-3 from Arabidopsis thaliana and similar sequences from plants. AtS40-3 is induced during senescence and is also regulated in response to dark treatment, ABA, salicylic
acid and pathogen attack . It also affects the natural variation of cyst nematodes sex ratio and susceptibility to parasitic nematodes, depending on single nucleotide polymorphism (SNPs) between cultivars .
ssRNA positive strand viral 18kDa cysteine-rich protein (Viral_P18)
Type: Family

This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.

This entry includes Suppressor of RNA silencing

. This protein is a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that performs sequence-specific inhibition of viral mRNAs expression .
Broad bean mottle virus, Gp1, N-terminal (BBMV_Gp1_N)
Type: Domain

This region represents the N-termini of Broad bean mottle virus, Gp1 (2a protein), and is always found N-terminal to a predicted RNA dependent RNA polymerase region (

).
Herpesvirus tegument protein U30 (Herpes_U30)
Type: Family

This family is named after the human herpesvirus protein, but has been characterised in cytomegalovirus as UL47. Cytomegalovirus UL47 is a component of the tegument, which is a protein layer surrounding the viral capsid. UL47 co-precipitates with UL48 and UL69 tegument proteins, and the major capsid protein UL86. A UL47-containing complex is thought to be involved in the release of viral DNA from the disassembling virus particle .
LURP-one-related (LOR)
Type: Family

The structure of protein LURP-one-related 15 (At5g01750) has been solved. It comprises a 12-stranded β-barrel with a central C-terminal α-helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein . In plants LURP1 plays a role in defense against pathogens .
Retinin-like protein (Retinin_C)
Type: Family

This entry consists of a number of Drosophila proteins which share a conserved C-terminal region related to that of the fly Retinin protein.
Adenovirus E4 30/34kDa protein (Adenovirus_E4_30/34)
Type: Family

This entry describes early region 4 open reading frame 3 (E4 ORF3) proteins, including E4 30k, 31k, 33k and 34k proteins.

Adenoviruses E4 is essential for DNA replication and late protein synthesis . The adenovirus E4 ORF3 protein is required for viral DNA replication during the interferon (IFN)-induced antiviral state .

The E4 ORF3 protein reorganises the promyelocytic leukemia (PML) protein nuclear bodies. These normally punctate structures are reorganised by E4 ORF3 into tracks that eventually surround viral replication centres. PML rearrangement is an evolutionarily conserved function of E4 ORF3 .

The product of adenovirus early region 4 (E4), open reading frame 6, is E4 34k. It modulates viral late gene expression, DNA replication, apoptosis, double strand break repair, and transformation through multiple interactions with components in infected and transformed cells . Conservation of several cysteine and histidine residues among E4 34k sequences suggests the presence of a zinc binding domain, which is important for its function .
Herpesvirus U59/UL88 (Herpes_U59/UL88)
Type: Family

The proteins in this family have no known function. Cytomegalovirus UL88 is also a member of this family.
Viral beta C/D-like (Viral_beta_CD)
Type: Family

This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Herpesvirus UL87, N-terminal (Herpes_UL87_N)
Type: Domain

This domain is found at the N termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N-terminal to the UL87 (

), which has no known function.
Herpesvirus U44 (Herpes_U44)
Type: Family

This entry represents uncharacterised proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. They are named variously as U44, BSRF1, UL71, and M71. The entry also includes BSRF1.
Herpesvirus UL56 (Herpes_UL56)
Type: Family

In herpes simplex virus type 2, UL56 is thought to be a tail-anchored type II membrane protein involved in vesicular trafficking. The C-terminal hydrophobic region is required for association with the cytoplasmic membrane, and the N-terminal proline-rich region is important for the translocation of UL56 to the Golgi apparatus and cytoplasmic vesicles .
TPM domain (TPM_dom)
Type: Domain

TPM domain is named after its founding proteins: TLP18.3, Psb32 and MOLO-1.

In Arabidopsis, this domain is called the thylakoid acid phosphatase -TAP - domain and has a Rossmann-like fold . In plants, the family resides in the thylakoid lumen attached to the outer membrane of the chloroplast/plastid. It is active in the photosystem II .

In C. elegans, the MOLO-1 protein is an auxiliary subunit that positively modulates the gating of levamisole-sensitive acetylcholine receptors .
Herpesvirus UL55 (Herpes_UL55)
Type: Family

In infected cells, UL55 is associated with the nuclear matrix, and found adjacent to compartments containing the capsid protein ICP35. UL55 was not detected in assembled virions. It is thought that UL55 may play a role in virion assembly or maturation .
Brain-expressed X-linked protein (BEX)
Type: Family

This family includes the brain-expressed X-liked proteins (which include)human p75NTR-associated cell death executor), which may be a signalling adaptor molecule involved in p75NTR-apoptosis induced by nerve growth factor. It may be important in neurogenetic diseases .
RNA polymerase sigma-70 region 3 (RNA_pol_sigma70_r3)
Type: Domain

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .
Herpesvirus UL51 (Herpes_UL51)
Type: Family

UL51 protein is a virion protein. In Suid herpesvirus 1 (Pseudorabies virus), UL51 (

) was identified as a component of the capsid . In Human herpesvirus 1 (HHV-1) there is evidence for post-translational modification of UL51 .