SII-SWORD/CoKE huggingface dataset:
Topoisomerase I damage affected protein 11 (Tda11)
Type: Family

Tda11 was identified as a protein affecting topoisomerase I-induced DNA damage from a high-throughput screening . It is a potential Cdc28p substrate . Its function is not clear.
Ribosomal biogenesis factor (RBIS)
Type: Family

This entry represents ribosomal biogenesis factor RBIS from animals. It is a trans-acting factor in ribosome biogenesis required for efficient 40S and 60S subunit production .
Orofacial cleft 1 candidate gene 1 protein (OFCC1)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 125 and 276 amino acids in length. The family includes OFCC1 (orofacial cleft 1 candidate gene 1 protein), a potentially causal gene for orofacial cleft in humans . However, ablation of the gene had no effects in head development in mice . Mutations in the homologous Opo gene result in eye malformation in medaka fish .
Nucleolar protein Swm2 (Swm2)
Type: Family

Swm2 (Synthetic With MUD-2-delta protein2) binds Tgs1, an enzyme responsible for 2,2,7-trimethylguanosine (TMG) capping of small nuclear (sn) RNAs implicated in pre-mRNA splicing . Deletion of SWM2 impairs pre-mRNA splicing and ribosome biogenesis, exhibiting a similar phenotype to tgs1 mutant. Swm2 is required for trimethylation of spliceosomal snRNAs and the U3 snoRNA by Tgs1 .
Spindle pole component 29 (Spc29)
Type: Family

Spc29 is a component of the Spc-110 subcomplex and is required for the SPB (Spindle pole body) duplication. Spc29 acts as a linker between the central plaque component Spc42 to the inner plaque component Spc110 .
Lymphocyte transmembrane adapter 1 (LAX)
Type: Family

LAX is a family of proteins is found in chordates. LAX is membrane-associated and expressed in B cells, T cells, and other lymphoid-specific cell types. It down-regulates antigen-receptor signalling in T cells by inhibiting TCR-mediated p38 MAPK activation .
Musculoskeletal embryonic nuclear protein 1 (MUSTN1)
Type: Family

Musculoskeletal embryonic nuclear protein 1 (Mustn1 or Mustang) constitutes a family of short, approx 80 residue, proteins found in chordates. Mustn1 localises to the nucleus and specifically, spatially in mesenchymal cells of the developing limbs and tail as well as in the fracture callus, especially in periosteal osteoprogenitor cells, proliferating chondrocytes, and young active osteoblasts. It is highly expressed during embryogenesis and is necessary for both chondrocyte proliferation and differentiation . It is inactivated in most adult tissues with the exception of skeletal muscle and tendon where is acutely and differentially expressed during bone regeneration .
Protein Sop4 (Sop4)
Type: Family

Sop4 is an ER-membrane protein involved in the export of Pma1, possibly through the monitoring or assisting of Pma1 folding and acquisition of competence to enter vesicles .
Multidrug resistance efflux pump SepA (SepA)
Type: Family

SepA is a drug efflux protein involved in bacterial multidrug resistance. It is predicted to have four transmembrane domains .
Male-specific protein scotti (Soti)
Type: Family

Soti is a post-meiotically transcribed gene that is required in late spermiogenesis for normal spermatid individualisation. Besides, it is expressed in primary spermatocytes and round spermatids .
SWI5-dependent HO expression protein 3 (She3)
Type: Family

SWI5-dependent HO expression protein 3 (She3) is an adaptor protein that links Myo4, a nonessential type V myosin, to its cargo . Ash1 mRNA binds to the She2 protein and form a complex. The She2-mRNA complex then binds to the adaptor protein She3. She3 associates with Myo4, and the fully assembled complex moves along actin cables to the bud tip, where it inhibits mating type switching in daughter cells by repressing HO endonuclease expression . A similar mechanism involving the She proteins is thought to regulate the asymmetric distribution of IST2 mRNA .

Myo4 and She3, but not She2, are required for the inheritance of cortical ER in S. cerevisiae .
Testis development-related protein (TDRP)
Type: Family

TDRP is a family of proteins found in chordates. It is predominantly expressed in the testis, distributed in both cytoplasm and the nuclei of spermatogenic cells. It may act as a nuclear factor with an important role in spermatogenesis .
Gametogenetin (GGN)
Type: Family

Gametogenetin (GGN) is a family of proteins largely found in vertebrates. GGN reacts with POG in the maturation of sperm and is expressed virtually only in the testis. It is also expressed in lower levels in the oocyte and is required for the survival of pre-implantation embryos . GGN plays a role in male meiotic DNA double strand break repair . It is found to be associated with the intracellular membrane, binds with GGNBP1 and may be involved in vesicular trafficking .
She1 (She1)
Type: Family

She1 is a microtubule associated protein that binds microtubules in vitro and localises to mitotic spindles, cytoplasmic microtubules, and a ring structure at the bud neck . It has been shown to interact with components of the Dam1 (DASH) complex . She1 inhibits the dynein activity, and this inhibition is important to prevent excessive detachment of cytoplasmic microtubules, particularly in G1 cells .
Protein LYRIC (LYRIC)
Type: Family

LYRIC (Lysine-rich CEACAM1 co-isolated protein), also known as Astrocyte-elevated gene-1 (AEG-1), is a type-1b membrane protein with a single transmembrane domain and localises to the endoplasmic reticulum and the nuclear envelope. It is also found in the nucleolus, suggesting functional relationships between these two cellular compartments . It is found to be colocalised with tight junction proteins ZO-1 and occludin in polarised epithelial cells, suggesting that LYRIC is part of the tight junction complex . LYRIC has been shown to promote angiogenesis and tumour cell migration and invasion by activating the transcription factor NF-kappaB .
Sbe2/Sbe22, C-terminal domain (Sbe2/Sbe22_C)
Type: Domain

This entry represents a domain found at the C-terminal of Sbe2 and its paralogue, Sbe22 from budding yeast. They are involved in bud growth and yeast cell wall formation. They may be involved in the transport of cell wall components from the Golgi apparatus to the cell surface periphery . This domain is predicted to adopt a globular structure with similarity to TBC domains.
Regulator of rDNA transcription 14 (Rrt14)
Type: Family

Rrt14 is a nucleolar protein whose function is not clear. It was identified in a screen for mutants with decreased levels of rDNA transcription . It may be involved in ribosome biogenesis .
Nuclear receptor-interacting protein 1, repression domain 1 (NRIP1_RD1)
Type: Domain

Nuclear receptor-interacting protein 1 (also known as nuclear factor RIP140) modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1 . It also modulates transcriptional repression by nuclear hormone receptors and clock gene expression . It consists of four distinct autonomous repression domains .

This domain is the first (N-terminal) repression domain of nuclear receptor-interacting protein 1 .
Nuclear receptor-interacting protein 1, repression domain 2 (NRIP1_RD2)
Type: Domain

Nuclear receptor-interacting protein 1 (also known as nuclear factor RIP140) modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1 . It also modulates transcriptional repression by nuclear hormone receptors and clock gene expression . It consists of four distinct autonomous repression domains .

This domain is the second repression domain of nuclear receptor-interacting protein 1 .
Nuclear receptor-interacting protein 1, repression domain 3 (NRIP1_RD3)
Type: Family

Nuclear receptor-interacting protein 1 (also known as nuclear factor RIP140) modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1 . It also modulates transcriptional repression by nuclear hormone receptors and clock gene expression . It consists of four distinct autonomous repression domains .

This domain is the third repression domain of nuclear receptor-interacting protein 1 .
Nuclear receptor-interacting protein 1, repression domain 4 (NRIP1_RD4)
Type: Domain

Nuclear receptor-interacting protein 1 (also known as nuclear factor RIP140) modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1 . It also modulates transcriptional repression by nuclear hormone receptors and clock gene expression . It consists of four distinct autonomous repression domains .

This domain is the fourth (C-terminal) repression domain of nuclear receptor-interacting protein 1 .
Darcynin (Darcynin)
Type: Family

Darcynin family contains a group of bacterial proteins with unknown function.
Stabilizer of axonemal microtubules 4 (SAXO4)
Type: Family

This entry represents the homologues of Stabilizer of axonemal microtubules 4 (SAXO4, formerly PPP1R32). SAXO4 belongs to a class of SAXO proteins that contain multiple Mn motifs that bind longitudinally along a single protofilament . In such proteins, Mn motitfs are speced 40 residues apart, corresponding to an apparent internal repeat of 8 nm. Mn motif consists of a 5- to 6-residue helix flanked by a Tyr/Phe residue on one end and by a Ser/Thr on the other that binds the shoulder of the α-tubulin S9/S10 loop. SAXO4 interacts with TEKT1 and bridges the tektin bundle with tubulin protofilaments close to the inner junction of axonemal doublet microtubules .
Two-component-system connector protein SafA (SafA)
Type: Family

SafA (also known as B1500) is a connector protein acting in the bacterial two-component signal-transduction systems (TCSs). It connects the signal transduction between the two-component systems EvgS/EvgA and PhoQ/PhoP, by directly interacting with PhoQ and thus activating the PhoQ/PhoP system, in response to acid stress conditions .
Torovirinae spike protein (S_torovirinae)
Type: Family

Spike protein (also known as S protein) is a virus glycoprotein that mediates receptor binding, membrane fusion, and virus entry, and determines host range .
Outer capsid protein VP7 (Capsid_VP7)
Type: Family

Outer capsid protein VP7 is a reoviral protein that interacts with VP4 to form the outer icosahedral capsid . Outer capsids are involved directly in viral host interactions.
Small ribosomal subunit protein bTHX (Ribosomal_bTHX)
Type: Family

This entry includes small ribosomal subunit protein bTHX found in bacteria. bTHX (also known as Thx) forms part of the bacterial 30S ribosomal subunit. It fits into a cavity between multiple RNA elements in the top of the 30S subunit head and stabilises the organisation of these elements .
Required for respiratory growth protein 8, mitochondrial (Rrg8)
Type: Family

The function of Rrg8 (required for respiratory growth protein 8) is not clear. It is required for respiratory activity and maintenance and expression of the mitochondrial genome . It is also involved in the plasma membrane electron transport in S. cerevisiae .
Mediator complex subunit 26, C-terminal domain (Med26_C)
Type: Domain

This entry represents the C-terminal domain of subunit 26 of the Mediator complex in eukaryotes (Med26). Med19 and Med26 act synergistically to mediate the interaction between Mediator and REST, a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes . The C-terminal domain is critical and sufficient for its assembly into Mediator and its interaction with Pol II. The most highly conserved C-terminal amino acids are critical for these interactions because deletion of the last eight amino acids from the Med26 C terminus disrupted binding to Mediator and Pol II .
Mediator complex subunit 26, middle domain (Med26_Mid)
Type: Domain

This entry represents the middle domain of subunit 26 of Mediator (Med26). Med19 and Med26 act synergistically to mediate the interaction between Mediator and REST, a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes .
RBPJ-interacting and tubulin-associated protein 1 (RITA1)
Type: Family

RITA (RBPJ-interacting and tubulin-associated protein) is a highly conserved protein that binds to tubulin and shuttles between the cytoplasm and nucleus. It is responsible for export of RBP-J/CBF-1 from the nucleus, which modulates Notch-mediated transcription .
RAD51 interacting motif (RAD51_interact)
Type: Domain

This motif interacts with RAD51, a protein that plays an important role in mitotic and meiotic recombination, and in DNA repair . This motif is found C-terminal in RAD51-associated protein 1 (RAD51AP1) and 2 (RAD51AP2).
UPF0669 protein C6orf120 (UPF0669)
Type: Family

The function of C6orf120 protein is not clear. C6orf120 recombinant protein has been shown to induce apoptosis of Jurkat cells and primary CD4(+) T cells .
Protein of unknown function DUF4666 (DUF4666)
Type: Family

This family of proteins is found in plants. Proteins in this family are typically between 103 and 140 amino acids in length. There are two conserved sequence motifs: LQRS and FRR.

Proteins containing this domain includes Arabidopsis At1g15400 and At1g80180. At1g80180 is a MAPK kinase substrate that may play a role in the regulation of stomata patterning .
Phosphatase SCO2771 (Phosphatase_SCO2771)
Type: Family

Members of this family display phosphatase activity in vitro .
UPAR/Ly6 domain-containing protein Quiver-like (QVR-like)
Type: Family

Drosophila QUIVER protein (qvr), also known as SLEEPLESS protein or SSS, is a small (~15kDa) glycosylphosphatidylinositol (GPI)-anchored protein from the Ly-6 family required for homoeostatic regulation of sleep under normal conditions and following sleep deprivation . SSS is a novel potassium channel subunit that regulates the voltage-gated potassium channel Shaker (Sh) protein, a potassium channel which regulates the sleep . This interaction suppresses neuronal excitability and enables sleep . Besides the Sh modulation, SSS also antagonises nicotinic acetylcholine receptors (nAChRs) to reduce synaptic transmission and promote sleep .

This entry also includes paralogues of qvr called UPAR/Ly6 domain-containing proteins such as crim, rtv and bero from Drosophila melanogaster and the uncharacterised protein F46C5.4 from C.elegans.
NPR1/NH1-interacting protein (NPR1/NH1-interacting)
Type: Family

NIMIN1/3 are linked to the salicylic acid-dependent systemic acquired resistance response (SAR), a plant immune response . They interact via a motif at the C terminus with the regulatory protein NPR1 (also known as NIM1), a key regulator of SAR in Arabidopsis .

NH1 is the rice orthologue of NPR1, and NRR has been identified as an NH1 and NPR1 interactor . NH1 is a transcriptional co-activator that represses NH1-mediated activation. NRR homologues 1, 2 and 3 (RH1, RH2, and RH3) have also been reported to bind to, and repress to varying degrees, NH1-mediated transcriptional activation . RH1 and RH3, but not RH2, also effectively repress NH1-mediated transcriptional activation .
Protein of unknown function DUF4667 (DUF4667)
Type: Family

This family of proteins is found in fungi. Proteins in this family are typically between 172 and 313 amino acids in length.
Protein of unknown function DUF4668 (DUF4668)
Type: Family

This family of proteins is found in fungi. Proteins in this family are typically between 142 and 211 amino acids in length.
Linker for activation of T-cells family member 2 (LAT2)
Type: Family

The adaptor protein linker activator of T-cells 2 (LAT2), also called non-T-cell activation linker (NTAL), linker activator for B-cells (LAB) or Williams Beuren Syndrome critical region 5 (WBSCR5), is expressed in various myeloid and lymphoid cells . Given the wide expression pattern, it may modulate signalling in most types of leukocytes . It has been shown to be involved in immunoreceptor signaling , B cell activation , negative regulation of T cell activation , and regulation of mast cell physiology .
Phenol-soluble modulin alpha peptide (PSM_alpha)
Type: Family

S. aureus secretes four shorter (~20 amino acids, the alpha-type) and two longer (~40 amino acids, the beta-type) phenol-soluble modulin (PSM)-like peptide. This entry represents the alpha type PSM peptides. PSMs may recruit, activate and induce the lysis of human neutrophils. They stimulate the secretion of IL-8 and also have haemolytic activity during MRSA infection .
Outer spore wall protein 5 (Osw5)
Type: Family

The outermost cape of the fungal spore wall is made up of a polymer that contains cross-linked amino acid dityrosine, which is important for the stress resistance of the spore . The OSW family of proteins have been implicated in assembly of this protective dityrosine coat. This entry includes OSW5 and related proteins, such as lipid droplet organization protein LDO16 (which is also known as OSW5).
Prostate androgen-regulated mucin-like protein 1 (PARM1)
Type: Family

Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein present in most tissues, with high levels in the heart, kidney and placenta . It is induced and expressed in prostate after castration and may have a role in cell proliferation and immortalisation in prostate cancer . PARM-1 also contributes to ovulation and/or luteal function by acting as a novel regulator of progesterone metabolism .
MALE GAMETOPHYTE DEFECTIVE 1 (MGP1)
Type: Family

This entry includes Arabidopsis MALE GAMETOPHYTE DEFECTIVE 1 (MGP1), which is a F(A)d subunit of mitochondrial F(1)F(0)-ATP synthase essential for pollen formation .
Monopolar spindle protein 2 (Mps2)
Type: Family

Monopolar spindle protein 2 (Mps2) is a fungal transmembrane protein localised to the spindle pole body (SPB) . It is required for the insertion of the nascent SPB into the nuclear envelope and for the proper execution of spindle pole body (SPB) duplication . The interaction between Mps2 and Spc24 may contribute to the localisation of Spc24 and other kinetochore components to the inner plaque of the SPB .
MgtA leader peptide (MGTL)
Type: Family

Bacterial mRNAs often contain leader sequences that respond to specific metabolites or ions by altering expression of the associated downstream protein-coding sequences. This entry represents mgtA leader peptide (mgtL), which controls transcription elongation into the mgtA coding region in response to changes in cytosolic proline levels. When the levels of proline are low, this protein is not able to be translated and stem loop'C' forms in the mgtA 5' UTR which enables the transcription of the downstream mgtA gene .
Transmembrane protein TMEM132, N-terminal (TMEM132_N)
Type: Domain

This entry represents the N-terminal domain found in members of the transmembrane protein 132 family.

The transmembrane protein 132 family (TMEM132) consists of TMEM132A, TMEM132B, TMEM132C, TMEM132D, TMEM132E. These are transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes . TMEM132 members have been associated with panic disorders, anxiety and major depressive disorders .

TMEM132A may play a role in embryonic and postnatal development of the brain. It increased resistance to cell death induced by serum starvation in cultured cells. It regulates cAMP-induced GFAP gene expression via STAT3 phosphorylation .

These proteins consist of six globular domains: N-terminal

, 2nd

, 3rd

, 4th

, 5th

and 6th

. The latter three are a tandem of Ig-like domains .

represents the C-terminal region which includes a single transmembrane helix.
Transmembrane protein TMEM132, C-terminal (TMEM132_C)
Type: Domain

This entry represents the C-terminal domain found in members of the transmembrane protein 132 family. It folds into a single transmembrane helix.

The transmembrane protein 132 family (TMEM132) consists of TMEM132A, TMEM132B, TMEM132C, TMEM132D, TMEM132E. These are transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes . TMEM132 members have been associated with panic disorders, anxiety and major depressive disorders .

TMEM132A may play a role in embryonic and postnatal development of the brain. It increased resistance to cell death induced by serum starvation in cultured cells. It regulates cAMP-induced GFAP gene expression via STAT3 phosphorylation .

These proteins consist of six globular domains: N-terminal

, 2nd

, 3rd

, 4th

, 5th

and 6th

. The latter three are a tandem of Ig-like domains .

represents the C-terminal region which includes a single transmembrane helix.
Transmembrane protein family 132, middle domain (TMEM132_M)
Type: Domain

This presumed domain is found in members of the TMEM132 family.

The transmembrane protein 132 family (TMEM132) consists of TMEM132A, TMEM132B, TMEM132C, TMEM132D, TMEM132E. These are transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes . TMEM132 members have been associated with panic disorders, anxiety and major depressive disorders .

TMEM132A may play a role in embryonic and postnatal development of the brain. It increased resistance to cell death induced by serum starvation in cultured cells. It regulates cAMP-induced GFAP gene expression via STAT3 phosphorylation .

These proteins consist of six globular domains: N-terminal

, 2nd

, 3rd

, 4th

, 5th

and 6th

. The latter three are a tandem of Ig-like domains .

represents the C-terminal region which includes a single transmembrane helix.
Mitochondrial coiled-coil domain protein 1 (MCCD1)
Type: Family

This is a family of uncharacterised proteins known as mitochondrial coiled-coil domain protein 1 .
Proline-rich protein family 20 (PRR20)
Type: Family

This family of proteins is found in chordates. Proteins in this family are typically between 73 and 221 amino acids in length. There is a conserved AYV sequence motif.
Protein of unknown function DUF4670 (DUF4670)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.
Break repair meiotic recombinase recruitment factor 1 (Brme1)
Type: Family

Brme1 (also known as Meiok21) is a component of meiotic recombination bridges involved in meiotic double-strand break repair . The C-terminal domain of Brme1 physically interacts with the N-terminal domain of HSF2BP . BRME1 facilitates the loading of RAD51 and DMC1 recombinases onto DSBs (DNA double-strand breaks) through interaction with MEILB2/HSF2BP and replacing ssDNA binding proteins . Brme1 is highly expressed in mice testes and fetal ovaries. Knockout of Brme1 results in male mice infertility .
Protein NPAT, C-terminal domain (NPAT_C)
Type: Domain

Protein NPAT is required for progression through the G1 and S phases of the cell cycle, and for S phase entry . It regulates histone gene expression as well as nonhistone targets that influence competency for cell cycle progression .

This entry represents the C-terminal domain of NPAT.
Mitochondrial biogenesis regulation protein 1 (Mbr1)
Type: Family

The function of Mbr1 is not clear. It has a paralogue, Mbr3, also known as Isf1. They are serine-rich, hydrophilic proteins. Overexpression of Mbr1 and Mbr3 can suppress the growth defect of hap2, hap3 and hap4 mutants. They may be involved in mitochondrial functions and stress response .