SII-SWORD/CoKE huggingface dataset:
Small proline-rich protein 2 (SPRR2)
Type: Family

Small proline-rich (SPRR) proteins are structural components of the cornified cell envelope of stratified squamous epithelia. They are subdivided into three families: SPRR1, SPRR2, and SPRR3 .

This entry represents SPRR2, a family of small proteins rich in proline, cysteine and glutamate. They contain a tandemly repeated nonamer, PKCPEPCPP . They are components of the cornified envelope of keratinocytes .
Protein of unknown function, YrpD (YrpD)
Type: Family

This entry represents bacterial proteins that are typically between 236 and 351 amino acids in length. The member from Bacillus subtilis is named YrpD (UniProtKB:

).
Threonine synthase, N-terminal (Thr_synth_N)
Type: Domain

This domain is found at the N terminus of many threonine synthase enzymes . Threonine synthases catalyses the gamma-elimination of phosphate from L-phosphohomoserine and the beta-addition of water to produce L-threonine .
Neuroblastoma-amplified sequence, N-terminal (NBAS_N)
Type: Domain

This entry represents the N-terminal domain of the neuroblastoma-amplified sequence (NBAS). This domain can also be found at the N terminus of several WD40-containing proteins. NBAS from human is over-expressed in neuroblastoma cells .
CST complex subunit Ten1, animal and plant type (Ten1_animal_plant)
Type: Family

This entry represents the CST complex subunit Ten1 homologue from plants and animals . Even though the protein sequence similarity is very low between budding yeast Ten1 (

) and animal/plant Ten1, they are evolutionarily related. Ten1 is essential for telomere integrity and it negatively regulates telomerase activity .

Two distinct telomere capping complexes have evolved: CST complex in budding yeast and shelterin complex in vertebrates. Budding yeast CST is composed of Cdc13, Ten1 and Stn1 . The homologues of Ten1 and Stn1 have been identified in vertebrates and plants. The vertebrate CST complex does not appear to play a primary role in telomere protection, but may complement the function of shelterin complex .

Similar to budding yeast Ten1, mammalian Ten1 forms the CST complex with Stn1 homologue and binds to single strand DNA (ssDNA). However, unlike budding yeast CST, the binding of mammalian CST to ssDNA is not sequence specific. The mammalian CST complex may have both telomeric and non-telomeric functions .

In plants, the CST complex is structurally analogous to mammalian CST and it plays a role in chromosome end protection .
Cilia- and flagella-associated protein 77 (CFAP77)
Type: Family

Proteins in this entry have been found in flagella .
FACT complex subunit SPT16, N-terminal lobe domain (FACT-SPT16_Nlobe)
Type: Domain

This entry represents the N-terminal lobe domain of Spt16. Its structure is similar to the RuvC/RNase H family. It may act as a protein-protein interaction domain presumably with partners outside of the FACT complex . The C-terminal lobe of NTD is structurally similar to aminopeptidases, and the most highly conserved surface residues line a cleft equivalent to the aminopeptidase substrate-binding site in peptidase family M24 (

).

SPT16 is a component of the FACT (facilitator of chromatin transcription) complex, a general chromatin factor that acts to reorganise nucleosomes . In budding yeasts, the N-terminal domain (NTD) of SPT16 includes a smaller N-terminal lobe (residues 1-175) and a larger C-terminal lobe (residues 176-447).
Creatinase/Aminopeptidase P/Spt16, N-terminal (Creatin/AminoP/Spt16_N)
Type: Homologous_superfamily

This entry represents the N-terminal domain of creatinase and aminopeptidase P, and the N-terminal lobe domain of the FACT complex subunit Spt16.
Double Cache domain 3 (dCache_3)
Type: Domain

Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2 channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors.

This entry represents the double Cache domain 3 (dCache_3), which may be a result of single Cache domain 3 (sCache_3) duplication .
Periplasmic sensor-like domain superfamily (Sensor-like_sf)
Type: Homologous_superfamily

This superfamily represents an α(2)-β(2)-α(2)-β(3) domain found in the sensory domain of two-component sensor kinases , in the C-terminal of the uncharacterised protein YkuI and in the periplasmic region of LuxQ . It may be related to the PAS (Per/ARNT/Simple-minded) domain .
Protein LKAAEAR1 (LKAAEAR1)
Type: Family

This entry represents a group of eukaryotic proteins containing a conserved LKAAEAR sequence motif. They are typically between 119 and 235 amino acids in length.
Chondroitin proteoglycan 4 (CPG4)
Type: Domain

This entry represents a domain found in chondroitin proteoglycan 4 (CPG4).
3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain (HIBADH-like_NADP-bd)
Type: Domain

3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. This entry represents the NAD-binding domain of 3-hydroxyisobutyrate dehydrogenase related sequences, such as 6-phosphogluconate dehydrogenase, that adopts a Rossmann fold .
SIPAR domain (SIPAR)
Type: Domain

This domain is found in SIPAR (STAT3-Interacting Protein As a Repressor). SIPAR inhibits STAT3 activity by accelerating its dephosphorylation . STAT3 is a member of the STAT family (signal transducers and activators of transcription) that plays an esential role in cell growth and differentiation.
CST complex subunit CTC1 (CTC1)
Type: Family

In animals and plants, CTC1 is a component of the CST complex (consists of Ten1, Stn1 and CTC1), a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation .
Centrosomal CEP44 domain (CEP44_CC)
Type: Domain

Several proteins have been identified that localise to centrosomes and spindle poles, and they have been named accordingly to their molecular weight . This entry represents a coiled coil domain found in centrosomal protein of 44kDa (CEP44).
Stimulator of interferon genes protein (STING)
Type: Family

Stimulator of interferon genes protein (STING) or endoplasmic reticulum interferon stimulator (ERIS, also known as Transmembrane protein 173 in human), is a transmembrane adaptor protein which is involved in innate immune signalling processes. It induces expression of type I interferons (IFN-alpha and IFN-beta) via the NF-kappa-B and IRF3, pathways in response to non-self cytosolic RNA and dsDNA . In addition to promote the production of type I interferons, members of this family play a direct role in autophagy .
Ribosome biogenesis protein C1orf109-like (CA109-like)
Type: Family

Ribosome biogenesis protein C1orf109 is involved in the cytoplasmic maturation steps of pre-60S ribosomal particles by promoting the release of shuttling protein RSL24D1/RLP24 from the pre-ribosomal particles . It has been first identified as the downstream target of a protein kinase, casein kinase 2 (CK2) which is upregulated in cancer cells. C1orf109 has been found upregulated in cancer cells and therefore, it has been suggested to be important in the regulation of cancer cell proliferation. The precise mechanism of CK2 targeting C1orf109 is not well characterised. It is found to be localised in the nucleus and cytoplasm .
Ubiquinol-cytochrome-c reductase complex assembly factor 4 (UQCC4)
Type: Family

This family includes ubiquinol-cytochrome-c reductase complex assembly factor 4 (UQCC4), a family of proteins that was discovered in a screen of Bos taurus placental ESTs. The B. taurus member of this family was named cattle cerebrum and skeletal muscle-specific transcript 1 (CCSMST1) , hence the alternative name of the family. This family of proteins is found in metazoa, both in vertebrates and invertebrates. Proteins are typically between 97 and 157 amino acids in length with a single completely conserved residue D that may be functionally important. UQCC4 is required for the assembly and stability of the mitochondrial ubiquinol-cytochrome c reductase complex (complex III (CIII) or cytochrome b-c1 complex), a multisubunit transmembrane complex that is part of the mitochondrial electron transport chain (ETC) which drives oxidative phosphorylation .
Spermatogenesis-associated protein 16 (SPATA16)
Type: Family

NYD-SP12, also known as SPATA16, is a germ-cell specific participant in the Golgi apparatus, and its expression is confined to spermatogenic epithelium, not being found in interstitial cells . Computer analysis of the protein-sequence showed that NYD-SP12 contains a cluster of phosphorylation sites for protein kinase C as well as for cyclic nucleotide-dependent protein kinases . It has been postulated that, since the mutation of some Golgi apparatus proteins is responsible for male infertility, NYD-SP12 might play a role in modification and sorting of acrosomal enzymes .
TRP-interacting helix, InaF motif (InaF-motif)
Type: Conserved_site

This highly conserved motif is thought to be a transmembrane helix that binds to transient receptor potential (TRP) calcium channel. It is found in proline-rich protein 24 (PRR24) and in InaF proteins. It is known that proline-rich proteins inactivate tannins found in food compounds, and it is thought that PRR24 does too. This is important since tannins often inhibit the uptake of iron . InaF is a protein required for TRP calcium channel function in Drosophila . TRP-related channels have been suggested to mediate "store-operated" calcium entry, important for Ca2+ homeostasis in a wide variety of cell types .
Histone deacetylase complex subunit SAP25 (SAP25)
Type: Family

In mammals, SAP25 is involved in the transcriptional repression mediated by the mSIN3 complex, which consists of at least SAP30, SAP45/Sds3, SAP130, SAP180/BCAA, RBP1, HDAC1 (histone deacetylase1), HDAC2, RbAp46, and RbAp48 . The mSIN3 complex can be recruited by sequence-specific DNA binding transcription factors and chromatin-binding proteins to specific regions of the genome and regulate their transcription . SAP25 binds to the the PAH1 domain of mSin3A and changes the conformation of the complex that affects its protein-protein interaction . SAP25 can be actively exported from the nucleus to cytoplasm by a CRM1-dependent nuclear export pathway. Its localisation is regulated by promyelocytic leukemia protein (PML), which induces a nuclear accumulation of SAP25 .
Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y (PIG-Y)
Type: Family

This entry represents the subunit Y of the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex found in the endoplasmic reticulum. The GPI-GnT complex catalyses the first step in the production of GPI (glycosylphosphatidylinositol)-anchors for cell surface proteins. PIG-Y may regulate activity of the complex by binding the catalytic subunit, PIG-A . In the absence of PIG-Y activity, the cell surface levels of GPI-anchored proteins are severely decreased .
Spermatogenesis-associated serine-rich protein 1 (SASRP1)
Type: Family

Spermatogenesis-associated serine-rich protein 1 (SRSP1) is a serine-rich protein differentially expressed during spermatogenesis .
Williams-Beuren syndrome chromosomal region 28 protein homologue (WBS28)
Type: Family

Transmembrane protein 270, also known as WBS28, is an integral membrane protein. These proteins have been identified as being linked to Williams-Beuren syndrome, which is a neurodevelopmental and multisystemic disease that is characterised by mental retardation with unique cognitive and personality profile and multiple dysmorphic and metabolic features . This family is found in eukaryotes and proteins are typically 266 amino acids in length.
Meiotically up-regulated gene 117 protein (Mug117)
Type: Family

This protein was identified as being up-regulated during meiosis in Schizosaccharomyces pombe, where it is required for correct meiotic chromosome segregation . This family of proteins is found in largely in plants and fungi. Proteins in this family are typically between 128 and 920 amino acids in length.
Meiotic recombination protein REC114-like (REC114L)
Type: Family

REC114-like is necessary for meiotic DNA double-strand break formation. It works in conjunction with Mei4 . This family of proteins is found in eukaryotes.
PEST proteolytic signal-containing nuclear protein (PCNP)
Type: Family

PCNP is a PEST-containing nuclear protein that is ubiquitinated by NIRF, a Np95/ICBP90-like RING finger protein probably involved in cell cycle regulation . PEST sequences, which are rich in proline (P), glutamic acid (E), serine (S) and threonine (T), are found in a number of short-lived proteins, such as transcription factors and cell cycle-associated proteins. Their function is generally controlled by proteolysis, mostly via ubiquitin-mediated degradation . NIRF and PCNP may constitute a novel signaling pathway with some relation to cell proliferation.
FAM180 family (FAM180)
Type: Family

This family of proteins of unknown function is found in eukaryotes. Proteins in this family are typically between 117 and 182 amino acids in length. There are two conserved sequence motifs: ELAS and DFE.
Protein of unknown function DUF4638 (DUF4638)
Type: Family

This entry represents a group of eukaryotic proteins that are typically between 240 and 272 amino acids in length. Their function is not known.
Putative testis-specific prion protein (PRNT)
Type: Family

Prion protein (PrP) is intimately linked with transmissible spongiform encephalopathies (TSEs). The human PrP gene (PRNP) locus contains three genes: PRNP, DOPPEL and PRND. A novel gene, designated PRNT, has been identified 3kb 3' to PRND and is transcribed to generate at least three alternatively spliced mRNAs. PRNT constitutes a family of putative prion-related proteins expressed in the testis . This group of eukaryotic proteins are typically between 52 and 94 amino acids in length.
Transmembrane protein family 171 (TMEM171)
Type: Family

This entry represents a group of eukaryotic proteins, TMEM71 (also known as parturition-related protein 2). They are typically between 242 and 326 amino acids in length.
Domain of unknown function DUF4637 (DUF4637)
Type: Domain

This domain is found in a group of eukaryotic proteins that are typically between 142 and 178 amino acids in length.
Exocyst complex component EXOC2/Sec5 (EXOC2/Sec5)
Type: Family

This entry includes Sec5 from yeasts and EXOC2 from animals.
Spermatogenesis-associated protein 24 (SPATA24)
Type: Family

This family of proteins bind to DNA and to TBP (TATA box binding protein), TATA-binding protein (TBP)-related protein 2 (TRF2) and several polycomb factors. It is likely to function as a transcription regulator .
Interferon lambda (INF_lambda)
Type: Family

Interferon (IFN)-lambda proteins belong to the new type III IFN group. In contrast to type I or type II IFNs, the response to type III IFN is cell-type specific. Only epithelial-like cells and some immune cells respond to IFN-lambda . In human,four distinct proteins called IFN-lambda1 (interleukin-29, IL-29), IFN-lambda2 (IL-28A), IFN_lambda3 (IL-28B) and IFNL4 have been identified . IFN-lambda proteins activate IFN-stimulated gene factor 3 (ISGF3), and are capable of inducing antiviral protection and MHC class I antigen expression .
Extracellular mutant protein 11, C-terminal (Ecm11_C)
Type: Domain

This entry represents the C-terminal domain of Ecm11 (extracellular mutant protein 11).
Mitochondrial import receptor subunit TOM5, metazoa (TOMM5_metazoa)
Type: Family

In budding yeasts, Tom5 forms part of the pre-protein translocase complex of the outer mitochondrial membrane (TOM complex) . This family is found in metazoans. Proteins in this family are homologues of yeast Tom5 and are approximately 50 amino acids in length.
Myc target protein 1 (Myc_target_1)
Type: Family

Myc target protein 1 (MYCT1) is regulated by the c-Myc oncoprotein; its promoter is a direct c-Myc target. Furthermore, MYCT1 regulates the expression of several other c-Myc target genes .
Barttin (Barttin)
Type: Family

Barttin is a beta-subunit for ClC-Ka and ClC-Kb chloride channels, with which it co-localises in basolateral membranes of renal tubules and of potassium-secreting epithelia of the inner ear . Mutations in Barttin gene cause Bartter syndrome 4A (BS4A), which is an autosomal recessive disorder characterised by impaired salt re-absorption in the thick ascending loop of Henle with pronounced salt wasting, hypokalemic metabolic alkalosis, and varying degrees of hypercalciuria.
Mitochondrial import receptor subunit TOM6 homologue (TOMM6)
Type: Family

In budding yeasts, Tom6 forms part of the pre-protein translocase complex of the outer mitochondrial membrane (TOM complex) . This family is found in metazoans. Proteins in this family are homologues of the yeast Tom6, and are typically between 43 and 74 amino acids in length.
C-X-C motif chemokine 17 (CXCL17)
Type: Family

C-X-C chemokine 17 (CXCL17) or dendritic cell and monocyte chemokine-like protein (DMC), is a cytokine-like protein that regulates recruitment of nonactivated blood monocytes and immature dendritic cells into tissues . It may play a role in the innate defense against infections . It also plays a role in angiogenesis and possibly in the development of tumours .
Something about silencing protein 4 domain (Sas4_dom)
Type: Domain

This entry represents a domain found in Sas4 (something about silencing protein 4).

SAS4 is a fungal silencing regulator. In S. cerevisiae, Sas4 is a subunit of a histone acetyltransferase complex termed SAS complex, which consists of Sas2, Sas4 and Sas5 . The SAS complex acetylates both free histones and nucleosomes and is involved in transcriptional silencing. Both Sas4 and Sas5 are required for optimal Sas2 histone acetyltransferase activity .
CMT1A duplicated region transcript 4 protein (CDRT4)
Type: Family

Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common inherited peripheral neuropathy and one of the best-characterised examples of a submicroscopic genomic disorder. In most cases it is due to a submicroscopic duplication of the 1.4-Mb genomic region in chromosome band 17p12. This putative protein represents the product of transcript 4 in this region .
Peroxisomal testis-specific protein 1 (PXT1)
Type: Family

This family of proteins is testis-specific .
Follicular dendritic cell secreted peptide (FDC-SP)
Type: Family

Follicular dendritic cells (FDCs) are cells of the immune system found in lymph follicles. They play a central role in the organisation of the follicular structure that supports B cell survival, affinity maturation of Ab responses, and the generation of long-lived B cell memory. Follicular dendritic cell secreted peptide (FDC-SP) is a novel secreted protein expressed by follicular dendritic cells. Its role is unknown, but it has been suggested that it may regulate immune responses .
Ribosomal RNA-processing protein 14, N-terminal (Rrp14_N)
Type: Domain

This entry represents the N-terminal domain of the Rrp14 (ribosomal RNA-processing protein 14) protein.
Thymic stromal lymphopoietin (TSLP)
Type: Family

Thymic stromal lymphopoietin (TSLP) is a cytokine that functions mainly on myeloid cells; it induces the release of T cell-attracting chemokines from monocytes and enhances the maturation of CD11c(+) dendritic cells . TSLP has proliferative effects on the myeloid cell line and may initiate asthma or atopic dermatitis responses by directly activating mast cells .
Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain (Rrp14/SURF6_C)
Type: Domain

This entry represents the C-terminal domain of the ribosomal RNA-processing protein 14 (Rrp14), which shares protein sequence similarity with surfeit locus protein 6 (SURF6).

In mammals, SURF6 is a component of the nucleolar matrix and has a strong binding capacity for nucleic acids . SURF6 is always found in the nucleolus regardless of the phase of the cell cycle suggesting that it is a structural protein constitutively present in nucleolar substructures. A role in rRNA processing has been proposed for this protein.
Up-regulated during septation protein 1 (Uds1)
Type: Domain

This entry represents a domain found in fungal proteins, including Uds1 (Up-regulated During Septation 1) from Schizosaccharomyces pombe. Uds1 is involved in septation . Many of the uncharacterised proteins with this domain are listed as being involucrin repeat proteins, but this can not be substantiated.
Spermatogenesis-associated protein 25 (SPATA25)
Type: Family

This family of proteins may be involved in spermatogenesis .
Testis-expressed sequence 12 protein (TEX12)
Type: Family

TEX12 is a meiosis-specific protein . TEX12 contributes to the formation of the central element of the synaptonemal complex (SC) in mouse meiocytes .
Lens epithelial cell protein LEP503 (LEP503)
Type: Family

This protein may be involved in lens epithelial cell differentiation .
Host cell factor C1 regulator 1 (HCFC1R1)
Type: Family

VP16 is a component of virion tegument layer that is required for the transcription of the viral immediate-early (IE) genes. In case of human herpes simplex virus (HSV) infection, VP16 binds to HCF-1 (host cell factor 1) and translocates to the nucleus to form a complex with the POU domain protein Oct-1. This complex then directs high level IE gene transcription by the potent activation domain in the C terminus of VP16. HCF-1 provides two functions required by VP16, complex assembly and nuclear targeting .
HUWE1-associated protein modifying stress responses-like (HAPSTR1-like)
Type: Family

This entry represents the HUWE1-associated protein modifying stress responses (HAPSTR1), also known as telomere attrition and p53 response 1 protein (TAPR1) from eukaryotes, including TAPR1 from human, which is a key multi stress-responsive protein that functions as a negative regulator of TP53/P53 in the cellular response to telomere erosion and probably also DNA damage. It functions in cooperation with the E3 ubiquitin ligase HUWE1 which also promotes TAPR1's degradation . HAPSTR2 plays a central regulatory role in the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding together with HAPSTR1 by stabilizing HAPSTR1, but also independently of HAPSTR1. This family also includes the uncharacterised proteins from fungi, such as YJR056C from yeast.
Cytoskeleton-associated protein 2, C-terminal (CKAP2_C)
Type: Domain

This entry represents the C terminus of CKAP2 (cytoskeleton-associated protein 2) and CKAP2L (cytoskeleton-associated protein 2-like). Mouse CKAP2 has been shown to possess microtubule stabilising properties and is involved in regulating aneuploidy, cell cycle, and cell death in a p53-dependent manner . In human, CKAMP2 is up-regulated in primary gastric cancers . It has been shown that human CKAP2 is degraded by APC/C-Cdh1 during mitotic exit and that a tight regulation of CKAP2 protein level is important for mitotic progression .
AJAP1/PANP, C-terminal (AJAP1_PANP_C)
Type: Domain

This is a domain found in the C terminus of adherens junction-associated protein 1 (AJAP1) and of PILR-associating neural protein (PANP). AJAP1 inhibits cell adhesion and migration . PANP is a ligand for the immune inhibitory receptor paired immunoglobulin-like type 2 receptor alpha .
THRAP3/BCLAF1 family (THRAP3_BCLAF1)
Type: Family

This family includes thyroid hormone receptor-associated protein 3 (THRAP3), which is a spliceosome component and a subunit of the TRAP complex which plays a role in pre-mRNA splicing and mRNA decay . It also includes the transcriptional repressor Bcl-2-associated transcription factor 1 (BCLAF1) .
Transmembrane protein 247 (TMEM247)
Type: Family

This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 197 and 222 amino acids in length. The function of this family is unknown.
Jiraiya (Jiraiya)
Type: Family

The membrane protein Jiraiya from Xenopus inhibits bone morphogenetic protein (BMP) signalling during embryogenesis . The human member of this family is uncharacterised protein TMEM221 (transmembrane protein 221).