SII-SWORD/CoKE huggingface dataset:
Dynein axonemal assembly factor 6 (DNAAF6)
Type: Family

Dynein axonemal assembly factor 6 is part of a complementary conserved R2TP-like HSP90 co-chaperone complex . The complex is required for cytoplasmic preassembly of flagellum axonemal dynein in spermatogenic cells, and therefore is required for sperm motility .
Uncharacterised protein C3orf38 (DUF4518) (UPF_C3orf38)
Type: Family

Proteins in this family are not characterised. They might be involved in apoptosis regulation .
Exosome complex RNA-binding protein 1/RRP40/RRP4 (Exosome_RNA_bind1/RRP40/RRP4)
Type: Family

This family includes archaeal probable exosome complex RNA-binding protein 1, exosome complex component RRP40 and RRP4. They are subunits of either archaeal or eukaryotic exosome complex. Exosome is a complex of 3' --> 5' exoribonucleases that play a major role in diverse RNA processing and degradation pathways.

The eukaryotic exosome complex contains 9 proteins. Six RNase PH domain containing proteins (Rrp41, Rrp42, Rrp43, Rrp45, Rrp46, and Mtr3) form a catalytic ring, three RNA binding domain containing proteins (Rrp4,Rrp40, and Csl4) bind on top of the ring .

In the archaeal exosome, the hexameric ring is formed by three dimers of the orthologs of Rrp41 and Rrp42 and degrades poly(A) RNA phosphorolytically. Three proteins with RNA binding domains (orthologues of Rrp4 or Csl4) bind to the ring and influences degradation of a short poly(A) RNA substrate by the hexameric ring .
Coiled-coil domain-containing protein 142 (CCDC142)
Type: Family

This entry contains coiled-coil domain-containing proteins. Their function is not known.
Coiled-coil domain-containing protein 83 (CCDC83)
Type: Family

This family consists of uncharacterised coiled-coil domain-containing proteins.
Glutamate-rich protein 2 (ERICH2)
Type: Family

This family consists of a group of uncharacterised proteins.
Katanin-interacting protein (KATNIP)
Type: Family

KATNIP is a microtubule-associated ciliary base protein probably involved in microtubule regulation .
Hid-1/Ecm30 (Hid-1/Ecm30)
Type: Family

Hid-1 (high-temperature-induced dauer-formation protein 1) was originally identified as a Caenorhabditis elegans gene encoding a protein that regulates larval development . HID-1 is conserved from fungi to humans. It contains up to seven potential transmembrane domains separated by regions of low complexity. It may control the correct sorting of DCV (dense core vesicle, also known as the secretory granule) cargoes in the Golgi apparatus .
Centrosome and spindle pole associated protein 1 (CSPP1)
Type: Family

Centrosome and spindle pole associated protein 1 (CSPP) interacts with MyoGEF (a guanine nucleotide exchange factor that localises to the central spindle and cleavage furrow) and may play a role in cell-cycle-dependent microtubule organisation .
Protein male-specific lethal-1 (Msl-1)
Type: Family

Protein male-specific lethal-1 (Msl-1) is a component of a multisubunit histone acetyltransferase complex (MSL). The MSL complex has histone acetyltransferase (HAT) activity with specificity towards histone H4 lysine 16 . In fruit fly, the MSL proteins are essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation). It has been shown that Msl-1 is associated with hundreds of discrete sites along the length of the X chromosome in males and not in females, and is also associated with 10-20 autosomal sites in males in fruit fly .

In humans the MSL complex has the same specificity for acetylating lysine 16 on histone H4, but in contrast to the Drosophila complex, the hMSL complex targets all chromosomes in vivo . In mammals the Msl-1 homologue is also known as hampin .
CRACD-like (CRACD-like)
Type: Family

This entry includes CRACD-like (also known as KIAA1211L) and KIAA1210 proteins. Their function is not known.
Small acidic protein (SMAP)
Type: Family

SMAP (small acid protein) family consists of small (~20kDa) glutamic acid-rich or aspartic acid-rich proteins. Homologues are known from metazoa and fungi.
Speriolin (SPATC1)
Type: Family

Speriolin is a sperm centrosome protein that form a complex with CDC20, CDC27 and TUBG1. It interacts with Cdc20 and is only detected in testis in humans . The function of speriolin and speriolin-like proteins is unknown.
PABIR1/2/3 (PBIR1/2/3)
Type: Family

This family represents the PPP2R1A-PPP2R2A-interacting phosphatase regulators (PABIRs), also known as FAM122 which includes PABIR1, PABIR2 and PABIR3 family members (FAM122A, B and C, respectively). The most studied member is PABIR1/FAM122A, which was identified as an inhibitor of serine/threonine-protein phosphatase 2A (PP2A) activity . It potentiates ubiquitin-mediated proteasomal degradation of serine/threonine-protein phosphatase 2A catalytic subunit alpha (PPP2CA) .
Spermatogenesis-associated protein 3 (SPATA3)
Type: Family

Spermatogenesis-associated protein 3 (SPATA3) is strongly expressed in testis in mice. It may have potential roles in spermatogenesis cell apoptosis or spermatogenesis .
Leucine zipper protein 2 (Luzp2)
Type: Family

The function of leucine zipper protein 2 (Luzp2) is not known. It is normally expressed only in brain and spinal cord .
Glutamate-rich protein 1 (ERICH1)
Type: Family

Proteins in this family are glutamate-rich proteins. Their function is unclear.
Cilia- and flagella-associated protein 91 (CFAP91)
Type: Family

CFAP91 (also known as AMY-1-associating protein expressed in testis 1 or AAT-1) is a component of a spoke-associated complex, regulates flagellar dynein activity by mediating regulatory signals between the radial spokes and dynein arms . It binds to AMY1 and may play a role in spermatogenesis .
Transmembrane protein 18 (TMEM18)
Type: Family

This entry represent the transmembrane protein 18 (TMEM18). In humans, TMEM18 is a transcription repressor and a sequence-specific ssDNA and dsDNA binding protein, with preference for GCT end CTG repeats . It enhances the tropism of neural stem cells for glioma cells .
Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 1/2 (NYAP1/NYAP2)
Type: Family

This entry includes NYAP1 and NYAP2 from neuronal tyrosine-phosphorylated adaptor for the PI 3-kinase (NYAP) family (consists of NYAP1, NYAP2, NAP3/Myosin16). NYAPs activate PI3K in PI3K pathway, which is a fundamental pathway for various cellular events in neurons. They also interact with components of the WAVE1 complex, which mediates actin cytoskeleton remodeling through Arp2/3 complex.
It was suggested that NYAPs connect PI3K activation to WAVE1 signalling in neurons
.
Bridge-like lipid transfer protein family member 3A/B (BLTP3A/B)
Type: Family

This family consists of bridge-like lipid transfer protein family member 3a/B (also known as UHRF1-binding protein 1 and 1-like proteins. These are tube-forming lipid transport proteins which mediate the transfer of lipids between membranes at organelle contact sites , and they are required for retrograde traffic of vesicle clusters in the early endocytic pathway to the Golgi complex .
Protein virilizer (Virilizer)
Type: Family

Protein virilizer may be involved in mRNA splicing regulation. Most of the studies on virilizer were carried out in fruit fly. In Drosophila, protein virilizer is required for male and female viability, sex determination and dosage compensation. It is involved in the female-specific splicing of Sxl transcripts. It is required for proper inclusion of regulated exons in Ubx transcripts .
Golgin subfamily A member 6-like (GOLGA6L)
Type: Family

Golgin are coiled-coil proteins localising in part of the Golgi stack. Some of the golgin members interact with small GTPase. They may have roles in membrane traffic and Golgi structure .
AP complex subunit beta (AP_beta)
Type: Family

Adaptor protein (AP) complexes function in protein transport via transport vesicles in different membrane traffic pathways. AP complexes are involved in the formation of clathrin-coated vesicles (CCVs) by recruiting the scaffold protein, clathrin. AP complexes are also involved in the cargo selection by recognising the sorting signals in proteins. Several AP complexes have been identified: AP-2 mediates endocytosis from the plasma membrane, while AP-1, AP-3 and AP-4 play a role in the endosomal/lysosomal sorting pathways . AP complexes are heterotetramers which consist of two large subunits, one medium subunit and one small subunit. One of the large subunits (alpha, gamma, delta and epsilon) mediates binding to the target membrane. The other large subunit (beta) recruits clathrin through the clathrin-binding sequence .
AP-3 complex subunit beta (AP3_beta)
Type: Family

The AP-3 complex functions in cargo-selective protein transport from the Golgi to the vacuole/lysosome . It is an adapter-related complex which is thought not to be clathrin-associated. The AP-3 complex facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to the vacuole. It is required for the transport via the ALP pathway . In neurons, AP-3 generates synaptic vesicles or vesicles carrying synaptic vesicle membrane proteins .

This entry represents the beta subunit of the AP-3 complex.
Protein strawberry notch (SNO)
Type: Family

Strawberry notch proteins carry DExD/H-box groups and helicase C-terminal domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes . Strawberry notch was first identified in Drosophila where functions downstream of Notch and regulates gene expression during development .

Protein FORGETTER 1 (included in this entry) is the A. thaliana orthologue of Strawberry notch .
Centrosomal protein kizuna (Centrosomal_kizuma)
Type: Family

Kizuna (is a Japanese word meaning "bond") is a centrosomal protein required for establishing a robust mitotic centrosome architecture that can endure the forces that converge on the centrosomes during spindle formation. It is required for stabilising the expanded pericentriolar material around the centriole . It can be regulated through phosphorylation by polo-like kinase 1 (Plk1) .
Sperm equatorial segment protein 1 (Equatorial_segment)
Type: Family

Equatorial segment protein (ESP) been localised to the equatorial segment of the acrosome in sperm. It defines a discrete acrosomal subcompartment that persists throughout acrosomal biogenesis and is required for fully fertile sperm .
Clarin (Clarin)
Type: Family

The clarin family consists of clarin-1, clarin-2 and clarin-3. Clarin-1 is a four-transmembrane protein expressed in cochlear hair cells and neural retina. It is also known as Usher syndrome type-3 protein, as mutations in the gene coding for this protein cause Usher syndrome type 3 (USH3), which is a genetically heterogeneous condition characterised by the association of retinitis pigmentosa and sensorineural deafness . It may have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells, and presumably also in analogous synapses within the retina . The function of clarin-2 and clarin-3 is not clear. Clarin-2 is predicted to adopt an α-β configuration.
Transmembrane protein 135 (Tmem135)
Type: Family

Transmembrane protein 135 (TMEM135) is a multi-pass membrane protein. It may be involved in fat storage and longevity regulation in Caenorhabditis elegans .
Protein N-terminal asparagine amidohydrolase (NTAN1)
Type: Family

Protein N-terminal asparagine amidohydrolase (NTAN1) acts on the side-chain deamidation of N-terminal asparagine residues to aspartate. It is required for the ubiquitin-dependent turnover of intracellular proteins that initiate with Met-Asn. These proteins are acetylated on the retained initiator methionine and can subsequently be modified by the removal of N-acetyl methionine by acylaminoacid hydrolase (AAH). Conversion of the resulting N-terminal asparagine to aspartate by PNAD renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. NTAN1 does not act on substrates with internal or C-terminal asparagines and does not act on glutamine residues in any position .
Cavin family (Cavin_fam)
Type: Family

This entry represents the cavin family (caveolae-associated proteins; previously known as the PTRF/SDPR family), which includes proteins cavin-1 to 4. They are critical regulators for caveolae dynamics . Caveolae are invaginations of the plasma membrane involved in many cellular processes, including clathrin-independent endocytosis, cholesterol transport, and signal transduction. Caveolins are the principal components of caveolae membranes. Polymerase I and transcript release factor (PTRF; also known as cavin-1) is essential for formation of caveolae and proper localisation of caveolins .
Pancreatic progenitor cell differentiation and proliferation factor (PPDPF)
Type: Family

Proteins in this family are probable regulators of exocrine pancreas development .
Protein FAM221A/B (Fam221a/b)
Type: Family

This family consists of functionally uncharacterised proteins.
Nucleolar and spindle-associated protein 1 (NuSAP)
Type: Family

Nucleolar and spindle-associated protein 1 (NuSAP) is a microtubule-associated protein with the capacity to bundle and stabilise microtubules . When overexpressed, it causes profound cytoplasmic microtubule bundling in interphase cells. It localises to the spindle during mitosis. NuSAP depletion by RNA interference results in defect in spindle midzone formation and aberrant anaphase and cytokinesis . NuSAP may be regulated by phosphorylation during mitosis . NuSAP is indispensable for mitosis and may play an important role in cancer progression and aggressiveness .
Endosome-associated-trafficking regulator 1 (ENTR1)
Type: Family

Endosome-associated-trafficking regulator 1 (ENTR1; also known as serologically defined colon cancer antigen 3, SDCCAG3) is important for protein trafficking and presentation of TNF receptor 1 on the cell surface . It is also involved in the regulation of cytokinesis and the formation of cilia .
Putative monooxygenase p33MONOX (P33MONOX)
Type: Family

Proteins in this family are potential NADPH-dependent oxidoreductases. In human, it interacts with COBRA1, NOL12 and PRNP and may be involved in the regulation of neuronal survival, differentiation and axonal outgrowth . It has been found down-regulated in the occipital lobe of an early stage Alzheimer's disease patients .
Spindle and kinetochore-associated protein 2 (Ska2)
Type: Family

Spindle and kinetochore-associated protein 2 (Ska2) is a component of the SKA1 complex (consists of Ska1, Ska2, and Ska3/Rama1), a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation . It is required for timely anaphase onset during mitosis, when chromosomes undergo bipolar attachment on spindle microtubules leading to silencing of the spindle checkpoint . The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies. The complex facilitates the processive movement of microspheres along a microtubule in a depolymerisation-coupled manner. In the complex, it is required for SKA1 localisation .
Transmembrane protein 182 (TMEM182)
Type: Family

Proteins in this entry are multi-pass membrane proteins. Their function is not clear.
Transmembrane protein 163 (Tmem163)
Type: Family

Transmembrane protein 163 (Tmem163) may bind zinc and other divalent cations and recruit them to vesicular organelles .
Protein FAM133 (Fam133)
Type: Family

This family consists of functionally uncharacterised proteins.
Transmembrane protein 151 (Tmem151)
Type: Family

Proteins in this family are multi-pass membrane proteins. Their function is not clear.
Yippee homolog double zinc finger protein (YPEH2ZP)
Type: Family

This entry represents a family of proteins (previously known as FAM72) that is distantly related to and named after the drosophila Yippee, a zinc-binding protein . In contrast to the other Yippee-like proteins (

,

,

) , this family of proteins possesses some distinct features such as the presence of a second putative zinc binding site that is unique to them. The constituent zinc coordinating residues of this second site are invariant within the family suggesting that this is likely a genuine zinc binding site.
MICOS complex subunit Mic13 (Mic13)
Type: Family

Mic13 (also known as Qil1) is a component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Mic13 is required for MICOS complex stability and cristae morphology .
Ribonuclease kappa (RNase_K)
Type: Family

Ribonuclease kappa is an endoribonuclease which preferentially cleaves ApU and ApG phosphodiester bonds. It hydrolyses UpU bonds at a lower rate . Its Ceratitis capitata homologue, also known as Cc RNase, exhibits ribonucleolytic activity against poly(C) and poly(U) synthetic substrates, as well as rRNA . RNase K (also known as V-type proton ATPase subunit f) regulates the activity of vacuolar (H+)-ATPase (V-ATPase) which is responsible for acidifying and maintaining the pH of intracellular compartments and required at an early stage of receptor-mediated endocytosis .
Transmembrane protein 218 (Tmem218)
Type: Family

Proteins in this family are multi-pass membrane proteins. Their function is not clear.
Fin bud initiation factor (Fibin)
Type: Family

Fin bud initiation factor (Fibin) forms disulfide-linked homodimers. It seems to also exist as monomers . It localises in endoplasmic reticulum and golgi apparatus . In zebrafish, Fibin is essential for the initiation of pectoral fin bud formation. It potentially acts downstream of retinoic acid and Wnt signaling and is required for tbx5 expression in the lateral plate mesoderm of presumptive pectoral fin bud regions . In mammals is expressed in cerebellum, skeletal muscle and other embryonic and adult tissues, suggesting a relevant role during embryogenesis and adult life .
Zygote arrest protein 1 (Zar1)
Type: Family

This family represents Zygote arrest protein 1 (ZAR1) and its homologues ZAR1-like proteins. ZAR1 is essential for female fertility and oocyte-to-embryo transition by coordinating maternal mRNA storage, translation and degradation . It is a mRNA-binding protein that mediates formation of MARDO (mitochondria-associated ribonucleoprotein domain), a membraneless compartment that stores maternal mRNAs in oocytes . MARDO assembly around mitochondria is directed by an increase in mitochondrial membrane potential during oocyte growth . ZAR1 binds to the 3'-UTR of maternal mRNAs . Maternal mRNAs stored in the MARDO are translationally repressed .
UPF0729 protein C18orf32-like (UPF0729_C18orf32-like)
Type: Family

This entry represents a family of uncharacterised proteins, including C18orf32 from human and its homologues. C18orf32 localises to the ER and lipid droplets (LDs) in the cell and has been described to be important for GPI-inositol deacylation. Mutations in this gene cause of a novel autosomal recessive neurodevelopmental disorder with hypotonia and contractures .
Plasma membrane fusion protein PRM1 (PRM1)
Type: Family

Plasma membrane fusion protein PRM1 is a fungi protein involved in cell fusion during mating by stabilising the plasma membrane fusion event .
MLLT11 family (MLLT11_fam)
Type: Family

This entry represents AF1q, encoded by the MLLT11 gene, which is a fusion partner of the MLL (mixed lineage leukemia) gene. The MLL-MLLT11 fusion is linked to the acute leukemias .

At the protein level, AF1q/MLLT11 is highly expressed in thymus and all leukemic cell lines, and is differentially expressed during neuronal differentiation . It interacts with the Notch signalling pathway to regulate the emergence of human prothymocytes . It has also been shown that AF1q increases radiation-induced apoptosis through up-regulation of BAD (BCL-2 antagonist of cell death) in human squamous carcinoma via NF-kappaB .
Calcium/calmodulin-dependent protein kinase II inhibitor (Camk2n)
Type: Family

This family includes calcium/calmodulin-dependent protein kinase II inhibitor 1 and 2 (CAMK2N1 and CAMK2N2). They are potent and specific inhibitor of CaM-kinase II (CAMK2) .
Proline-rich nuclear receptor coactivator 1/2 (PNRC1/2)
Type: Family

Proline-rich nuclear receptor coactivator 1 (PNRC1) and proline-rich nuclear receptor coactivator 2 (PNRC2) represent a new type of nuclear receptor co-regulatory proteins . PNRC1 may play a role in signal transduction . PNRC2 may be involved in nonsense-mediated mRNA decay (NMD) .
Protein FAM131 (FAM131)
Type: Family

This family represents a group of uncharacterised proteins known as FAM131.
Constitutive coactivator of PPAR-gamma (Coact_PPARg)
Type: Family

Constitutive coactivator of peroxisome proliferator-activated receptor (PPAR-gamma) functions as a transactivator of PPARG and ESR1. It functions in adipogenesis through PPARG activation .
Transmembrane protein 141 (Tmem141)
Type: Family

Proteins in this family are multi-pass membrane proteins. Their function is not clear.
Dedicator of cytokinesis (DOCK)
Type: Family

DOCK family members are evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases . DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis. The N-terminal SH3 domain of the DOCK proteins functions as an inhibitor of GEF, which can be relieved upon its binding to the ELMO1-3 adaptor proteins, after their binding to active RhoG at the plasma membrane . DOCK family proteins are categorised into four subfamilies based on their sequence homology: DOCK-A subfamily (DOCK1/180, 2, 5), DOCK-B subfamily (DOCK3, 4), DOCK-C subfamily (DOCK6, 7, 8), DOCK-D subfamily (DOCK9, 10, 11) . All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker).
Adipose-secreted signaling protein (ADISSP)
Type: Family

This family represents the adipocyte-secreted protein (adipokine) formerly known as UPF0687, that acts as a key regulator for white adipose tissue (WAT) thermogenesis and glucose homeostasis at least in part through activation of protein kinase A (PKA) . This protein is adipose-specific, highly expressed in brown adipose tissue.
Shiftless antiviral inhibitor of ribosomal frameshifting (SHFL)
Type: Family

This family describes shiftless antiviral inhibitor of ribosomal frameshifting protein (SHFL). SHFL has been shown to inhibit programmed -1 ribosomal frameshifting (-1PRF) in a variety of mRNAs from viruses (for example HIV1 GAG-POL) as well as cellular genes .

SHFL is also known as repressor of yield of DENV (RyDEN), and has been identified as a interferon-stimulated cellular inhibitor against Dengue Virus (DENV) and other viruses replication . It is likely to interfere with the translation of DENV via interaction with viral RNA and cellular mRNA-binding proteins.
HAUS augmin-like complex subunit 6 (HAUS_6)
Type: Family

This entry represents subunit 6 of the HAUS augmin-like complex, involved in mitotic spindle assembly, maintenance of centrosome integrity and completion of cytokinesis . Subunit 6 interacts with the NEDD1-gamma-tubulin complex and recruits this complex to the spindle, which in turn promotes microtubule polymerisation .

Although plant cells assemble the mitotic spindle in the absence of the centrosome structure, they also possess an augmin complex with similar functions in microtubule nucleation and organisation. The Arabidopsis augmin complex contains both conserved and unique subunits compared with its animal counterparts . This entry includes plant AUGMIN subunit 6 (AUG6).