SII-SWORD/CoKE huggingface dataset:
Sfmbt, SAM domain (Sfmbt_SAM)
Type: Domain

Drosophila Sfmbt (dSfmbt) is part of the Pho repressive complex (PhoRC) responsible for HOX (Homeobox) gene silencing. In this complex, Pho or Pho-like proteins bind DNA and dSfmbt binds methylated histones. dSfmbt contains a SAM (sterile alpha motif) domain and 4 MBT repeats. dSfmbt can interact with mono- and di-methylated histones H3 and H4 through the MBT repeats . It also interacts with the PcG protein Scm, a related MBT-repeat protein with similar methyl-lysine binding activity .

This entry represents the SAM domain, which is a putative protein-protein interaction domain.
Diacylglycerol kinase delta, SAM domain (DGK-delta_SAM)
Type: Domain

This entry represents the SAM domain of DGK-delta and similar proteins from vertebrates.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid.DGK-delta is a member of the diacylglycerol kinase family. DGK-delta is involved in the regulation of clathrin-dependent endocytosis . It is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis . The SAM domain of DGK-delta proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers with the SAM domain of DGK-eta proteins. The oligomerisation plays a role in the regulation of the DGK-delta intracellular localisation: it inhibits the translocation of the protein to the plasma membrane from the cytoplasm . The SAM domain also can bind Zn at multiple (not conserved) sites driving the formation of highly ordered large sheets of polymers, thus suggesting that Zn may play important role in the function of DCK-delta . DAG kinase delta also contains two copies of the C1 domain.
Diacylglycerol kinase (DGK)
Type: Family

Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. Upon cell stimulation, diacylglycerol kinase (DGK) converts DAG into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity . Most vertebrate species contain 10 different DGK isozymes. The catalytic domain constitutes the single largest sequence element within the DGK proteins that is commonly and uniquely shared by all family members . DGK proteins can be classified into five classes based on the presence or absence of specific functional domains. DGKs play an important role in controlling diverse cellular processes including development, cell division and proliferation, neuronal and immune responses, vascular traffic, apoptosis and cytoskeletal reorganization .
STIM1/2 (STIM1/2)
Type: Family

STIM1 (Stromal Interaction Molecule 1) is a key Ca2+ sensor located in the membrane of the endoplasmic reticulum (ER). Upon depletion of ER Ca2+ stores, STIM1 undergoes a conformational change and oligomerises, migrating to ER-plasma membrane junctions to activate Orai1, a Ca2+-release-activated Ca2+ (CRAC) channel, in the plasma membrane. STIM1 contains a single SAM (sterile alpha motif) domain (

) and an unpaired EF-hand domain (

) in the conserved luminal region, which together serve as a Ca2+-sensing module. These domains form a stable intramolecular complex when Ca2+ is bound. During Ca2+ depletion, destabilisation of the EF-SAM interaction leads to partial unfolding and promotes homooligomerisation, an essential step for CRAC channel activation . The cytoplasmic region includes coiled-coil domains that are conserved in structure and position and are necessary for interaction with Orai1 . In human cells, STIM1 and its homologue STIM2 regulate store-operated calcium entry (SOCE) as well as basal cytoplasmic Ca2+ levels .
Stromal interaction molecule 1, SAM domain (STIM1_SAM)
Type: Domain

Stromal interaction molecule 1 (STM1) is a single-pass transmembrane protein that spans the ER membrane, with its N-terminal region (STIM1-N, approximately 22kDa) located in the ER lumen . Upon store depletion, it serves as a Ca2+ sensor that activates Orai1, a CRAC (calcium-release-activated calcium) channel in the plasma membrane . CRAC channel is a store-operated calcium (SOC) influx channel that is important in Ca2+ signalling and many other cellular processes .

This entry represents the SAM domain of STIM1. SAM domain is a putative protein-protein interaction domain.
Stromal interaction molecule 2, SAM domain (STIM2_SAM)
Type: Domain

STIM1 (Stromal Interaction Molecule 1) is a key Ca2+ sensor located in the membrane of the endoplasmic reticulum (ER). Upon depletion of ER Ca2+ stores, STIM1 undergoes a conformational change and oligomerises, migrating to ER-plasma membrane junctions to activate Orai1, a Ca2+-release-activated Ca2+ (CRAC) channel, in the plasma membrane. STIM1 contains a single SAM (sterile alpha motif) domain (

) and an unpaired EF-hand domain (

) in the conserved luminal region, which together serve as a Ca2+-sensing module. These domains form a stable intramolecular complex when Ca2+ is bound. During Ca2+ depletion, destabilisation of the EF-SAM interaction leads to partial unfolding and promotes homooligomerisation, an essential step for CRAC channel activation . The cytoplasmic region includes coiled-coil domains that are conserved in structure and position and are necessary for interaction with Orai1 . In human cells, STIM1 and its homologue STIM2 regulate store-operated calcium entry (SOCE) as well as basal cytoplasmic Ca2+ levels .

This entry represents the SAM domain of STIM2.
Tumour protein p63, SAM domain (Tumor-p63_SAM)
Type: Domain

The transcription factor p63 shares protein sequence similarity with the tumour suppressor p53 . It plays an important part in maintaining the progenitor basal cell populations in stratified epithelium . It is also involved in heart development and human reproduction . Two p63 isoforms, the "trans-activating" isoforms and "truncated" isoforms, have been identified in humans. These isoforms may have different roles in skin, heart and germ line .

This entry represents the SAM domain of tumour protein p63. SAM domain is a putative protein-protein interaction domain. Mutations in the SAM domain of p63 are found in AEC (ankyloblepharonectodermal dysplasia-clefting) syndrome patients .
Tumour protein p73, SAM domain (Tumour-p73_SAM)
Type: Domain

Tumour protein p73 shares protein sequence similarity with the tumour suppressor p53 . It is involved in the apoptotic response to DNA damage . Human p73 has two isoforms, TA-isoforms that act as tumour-suppressors and DN-isoforms that behave as proto-oncogenes . p73 also plays a role in neuronal development and neurodegeneration .

This entry represents the SAM domain of tumour protein p73. The SAM domain of p73 has been shown to bind membrane lipids, and structural rearrangements in SAM are necessary to accomplish the binding .
Kazrin, SAM domain repeat 1 (Kazrin_SAM_rpt_1)
Type: Domain

Kazrin is a periplakin-interacting protein associated with desmosomes and the keratinocyte plasma membrane . In Xenopus embryos, loss of kazrin causes defects in cell adhesion that affect axial elongation, notochord differentiation and epidermal morphogenesis . The kazrin protein has several isoforms. Kazrin A, B, C and D are associated with cell junctions and embryonic development, while kazrin E is shown to interact with microtubules and involved in epidermal differentiation and desmosome formation. Kazrin F is involved in cervical cancer tumorigenesis .

The long isoform of kazrin contains three copies (repeats) of the SAM domain. This entry represents the repeat 1.
Kazrin (Kazrin)
Type: Family

Kazrin is a periplakin-interacting protein associated with desmosomes and the keratinocyte plasma membrane . In Xenopus embryos, loss of kazrin causes defects in cell adhesion that affect axial elongation, notochord differentiation and epidermal morphogenesis . The kazrin protein has several isoforms. Kazrin A, B, C and D are associated with cell junctions and embryonic development, while kazrin E is shown to interact with microtubules and involved in epidermal differentiation and desmosome formation. Kazrin F is involved in cervical cancer tumorigenesis .
Kazrin, SAM domain repeat 2 (Kazrin_SAM_rpt_2)
Type: Domain

Kazrin is a periplakin-interacting protein associated with desmosomes and the keratinocyte plasma membrane . In Xenopus embryos, loss of kazrin causes defects in cell adhesion that affect axial elongation, notochord differentiation and epidermal morphogenesis . The kazrin protein has several isoforms. Kazrin A, B, C and D are associated with cell junctions and embryonic development, while kazrin E is shown to interact with microtubules and involved in epidermal differentiation and desmosome formation. Kazrin F is involved in cervical cancer tumorigenesis .

The long isoform of kazrin contains three copies (repeats) of the SAM domain. This entry represents repeat 2.
Kazrin, SAM domain repeat 3 (Kazrin_SAM_rpt_3)
Type: Domain

Kazrin is a periplakin-interacting protein associated with desmosomes and the keratinocyte plasma membrane . In Xenopus embryos, loss of kazrin causes defects in cell adhesion that affect axial elongation, notochord differentiation and epidermal morphogenesis . The kazrin protein has several isoforms. Kazrin A, B, C and D are associated with cell junctions and embryonic development, while kazrin E is shown to interact with microtubules and involved in epidermal differentiation and desmosome formation. Kazrin F is involved in cervical cancer tumorigenesis .

The long isoform of kazrin contains three copies (repeats) of SAM domain. This entry represents the repeat 3.
Liprin-beta, SAM domain repeat 1 (Liprin-beta_SAM_rpt_1)
Type: Domain

Liprin-beta proteins contain three copies (repeats) of the SAM (sterile alpha motif) domain, which is a protein-protein interaction domain. This entry represents the repeat 1 domain. Liprin-beta may form heterodimers with liprin-alpha proteins through their SAM domains . Liprin beta1 has been shown to interacts with metastasis-associated protein S100A4 (Mts1), and this interaction results in the inhibition of liprin-beta-1 phosphorylation by protein kinase C and protein kinase CK2 in vitro .
Liprin-beta, SAM domain repeat 2 (Liprin-beta_SAM_rpt_2)
Type: Domain

This entry represents the SAM (sterile alpha motif) domain repeat 2 of liprin-beta. Liprin-beta proteins contain three copies (repeats) of the SAM domain, which is a protein-protein interaction domain. They may form heterodimers with liprin-alpha proteins through their SAM domains . Liprin beta1 has been shown to interacts with metastasis-associated protein S100A4 (Mts1), and this interaction results in the inhibition of liprin-beta-1 phosphorylation by protein kinase C and protein kinase CK2 in vitro .
Liprin-beta, SAM domain repeat 3 (Liprin-beta_SAM_rpt_3)
Type: Domain

This entry represents the SAM (sterile alpha motif) domain repeat 3 of liprin-beta protein. Liprin-beta proteins contain three copies (repeats) of SAM domain, which is a protein-protein interaction domain. They may form heterodimers with liprin-alpha proteins through their SAM domains . Liprin beta1 has been shown to interacts with metastasis-associated protein S100A4 (Mts1), and this interaction results in the inhibition of liprin-beta-1 phosphorylation by protein kinase C and protein kinase CK2 in vitro .
Liprin-alpha, SAM domain 1 (LIP-1_SAM_1)
Type: Domain

This entry represents the SAM (sterile alpha motif) domain repeat 1 of liprin-alpha.

Liprin-alpha proteins contain three copies (repeats) of the SAM domain, which is a protein-protein interaction domain. They may form heterodimers with liprin-beta proteins through their SAM domains (

,

,

). They participate in mammary gland development and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone .
Liprin-alpha, SAM domain 2 (LIP-1_SAM_2)
Type: Domain

This entry represents the SAM (sterile alpha motif) domain repeat 2 of liprin-alpha.

Liprin-alpha proteins contain three copies (repeats) of the SAM domain, which is a protein-protein interaction domain. They may form heterodimers with liprin-beta proteins through their SAM domains (

,

,

). They participate in mammary gland development and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone .
Liprin-alpha, SAM domain 3 (LIP-1_SAM_3)
Type: Domain

This entry represents the SAM (sterile alpha motif) domain repeat 3 of liprin-alpha.

Liprin-alpha proteins contain three copies (repeats) of the SAM domain, which is a protein-protein interaction domain. They may form heterodimers with liprin-beta proteins through their SAM domains (

,

,

). They participate in mammary gland development and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone .
SAMSN1, SAM domain (SAMSN1_SAM)
Type: Domain

SAMSN1 (also known as HACS1 or NASH1) is a member of the SH3/SAM adapter molecules family. It is strongly up-regulated in primary B cells upon differentiation and proliferation-inducing stimuli and functions as an endogenous immunoinhibitor. It has been found to regulate cell spreading and polarization . 14-3-3 proteins interact and control nucleo-cytoplasmic shuttling of SAMSN1. In the nucleus, SAMSN1 interacts with the SAP30/HDAC1 complex and regulates the activity of HDAC1 .

This entry represents the SAM domain of SAMSN1. The SAM domain is a predicted protein-protein interaction domain.
Nuclear pore complex protein Nup133-like (Nup133-like)
Type: Family

This entry includes the nuclear pore complex proteins Nup133, Nup132, Nup131 and Nup15 (from Caenorhabditis elegans). Nup133 is a component of the Nup160 subcomplex, which consists of Nup160, Nup133, Nup107 and Nup96, and is important for mRNA export from the nucleus . Nup160 subcomplexes are localized to both sides of the NPC during interphase. Nup133 also localizes to kinetochores . Nup131 and Nup132 are components of the npc107-120 complex in Schizosaccharomyces pombe. This complex consists of nup85, nup107, nup120, nup131, nup132 and seh1 and is also required for mRNA export .
Nucleoporin Nup37 (NUP37)
Type: Family

This entry includes nucleoporin Nup37, a component of the Nup107-160 subcomplex of the nuclear pore complex (NPC). Nup107-160 is required for assembly of a functional NPC, as well as normal kinetochore microtubule attachment, mitotic progression and chromosome segregation . The vertebrate Nup107-160 complex includes NUP160, NUP133, NUP107, NUP98, NUP85, NUP43, NUP37, SEH1 and SEC13 . This entry also includes some uncharacterised fungal proteins.
SASH1, SAM domain repeat 1 (SASH1_SAM_repeat1)
Type: Domain

This entry represents the SAM (sterile alpha motif) domain repeat 1 of SASH1, which is a predicted protein-protein interaction domain. SASH1 contains an SH3 domain and two SAM domains, and is a member of the SH3/SAM adapter molecules family. SASH1 has been identified as a tumour suppressor and critical protein in signal transduction .
SASH1, SAM domain repeat 2 (SASH1_SAM_repeat2)
Type: Domain

This entry represents the SAM (sterile alpha motif) repeat 2 of SASH1, which is a predicted protein-protein interaction domain. SASH1 is a member of the SH3/SAM adapter molecules family and has been identified as a tumour suppressor and critical protein in signal transduction .
ZCCH14, SAM domain (ZCCH14_SAM)
Type: Domain

The SAM (sterile alpha motif) domain of ZCCH14 (zinc finger CCHC domain-containing protein 14) is a putative RNA binding domain .
Protein Smaug, SAM domain (Smaug_SAM)
Type: Domain

Smaug participates in regulation of transcript stability and degradation . In Drosophila, Smaug is a translational repressor of the maternal mRNA of Nanos, a protein required for the formation of the anterior-posterior body axis. Repression depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. The SAM domain interacts specifically with the Nanos mRNA regulatory regions . Moreover, Smaug is also involved in regulation of specific maternal transcripts degradation in Drosophila early embryo via recruitment of the CCR4/POP2/NOT deadenylase .

This entry represents the SAM (sterile alpha motif) domain of Smaug, which is a C-terminal RNA binding domain. This domain interacts with stem-loop structures of mRNA .
VTS1, SAM domain (VTS1_SAM)
Type: Domain

VTS1 participates in regulation of transcript stability and degradation , and may be involved in vacuolar protein transport regulation . In budding yeasts, VTS1 induces mRNA degradation via the major deadenylation-dependent mRNA decay pathway; VTS1 recruits CCR4/POP2/NOT deadenylase complex to target mRNA. The recruitment is the initial step resulting in poly(A) tail removal transcripts .

The SAM (sterile alpha motif) domain of VTS1 is a C-terminal RNA binding domain. This domain interacts with stem-loop structures of mRNA .
EPH-B4, SAM domain (EPH-B4_SAM)
Type: Domain

The SAM domain of EPH-B4 is a potential protein-protein interaction domain . This domain is located in the cytoplasmic region of EPH-B4 receptors and appears to mediate cell-cell initiated signal transduction. EPH-B4 regulates blood vessel morphogenesis and patterning of the postnatal vascular systems . It has been implicated in human cancers .
Serine/threonine-protein kinase greatwall, catalytic domain (MASTL_STKc)
Type: Domain

The MASTL kinases carry only a catalytic domain, which contains a long insertion relative to MAST kinases. MASTL, also called greatwall kinase (Gwl), is involved in the regulation of mitotic entry, which is controlled by the coordinated activities of protein kinases and opposing protein phosphatases (PPs) . The cyclin B/CDK1 complex induces entry into M-phase while PP2A-B55 shows anti-mitotic activity. MASTL/Gwl is activated downstream of cyclin B/CDK1 and indirectly inhibits PP2A-B55 by phosphorylating the small protein alpha-endosulfine (Ensa) or the cAMP-regulated phosphoprotein 19 (Arpp19), resulting in M-phase progression . Gwl kinase may also play roles in mRNA stabilization and DNA checkpoint recovery . The human MASTL gene has also been named FLJ14813; a missense mutation in FLJ14813 is associated with autosomal dominant thrombocytopenia .
SMOC-1, extracellular calcium-binding domain (SMOC1_EC)
Type: Domain

SMOC-1 is predominantly localized in basement membranes . It acts as a regulator of osteoblast differentiation and is involved in the transforming growth factor-beta (TGF-beta) signaling . It also plays an essential role in ocular and limb development and functions as a regulator of bone morphogenic protein (BMP) signaling . Mutations of the SMOC-1 gene cause Waardenburg anophthalmia syndrome, a rare disorder presenting with ocular anomalies, ranging from mild microphthalmia to true anophthalmia, and limb anomalies.
.
SMOC-2, extracellular calcium-binding domain (SMOC2_EC)
Type: Domain

SMOC-2 is a ubiquitously expressed matricellular protein that enhances the response to angiogenic growth factors, mediate cell adhesion, keratinocyte migration, and metastasis . It is also associated with vitiligo and craniofacial and dental defects . Moreover, SMOC-2 acts as an Arf1 GTPase-activating protein (GAP) that interacts with clathrin heavy chain (CHC) and clathrin assembly protein CALM and functions in the retrograde, early endosome/trans-Golgi network (TGN) pathway in a clathrin- and AP-1-dependent manner .
SPARC, follistatin-like domain (SPARC_FS)
Type: Domain

SPARC (also known as BM-40 or osteonectin) is a matricellular protein essential for embryo development in invertebrates and highly expressed in bone . It participates in normal tissue remodeling as it regulates the deposition of extracellular matrix, as well as in neoplastic transformation . It is involved in extracellular matrix (ECM) assembly and fibrosis through binding both fibrillar collagen and basal lamina collagen IV . It regulates the activity of matrix metalloproteinases (MMPs), as well as the growth factor signaling mediated by cell surface receptors including vascular endothelial growth factor (VEGF) receptor, basic fibroblast growth factor (bFGF), and transforming growth factor (TGF) beta1. Overexpression of SPARC has been linked to cancers . SPARC is also a bone-associated protein that has a major role in bone development and mineralisation. It is involved in the initiation and progression of vascular calcification and upregulated by adiponectin . Furthermore, SPARC may be one of the molecules that govern the uptake and delivery of proteins from blood to the cerebrospinal fluid (CSF) during brain development .

SPARC contains an N-terminal acidic 52-residue segment followed by a follistatin-like (FS) domain, and an α-helical EC domain with 2 unusual calcium-binding EF-hands and the collagen-binding site . Platelet-derived growth factor (PDGF) interacts with its EC domain, but in a calcium-independent manner, whereas collagen binding is calcium-dependent .

This entry represents the FS domain of SPARC.
HERV-H LTR-associating protein 1 (HHLA1)
Type: Family

The function of HHLA1 is not clear. In teratocarcinoma cell lines, it has been shown to fuse with otoconin-90 .
Transcriptional activator MN1 (MN1)
Type: Family

MN1 is a transcription factor that regulates mammalian palate development and is required for appropriate osteoblast proliferation, motility, differentiation, and function . Its overexpression has been linked to acute myeloid leukemia (AML) poor prognosis .
Keratinocyte-associated transmembrane protein 2 (KCT2)
Type: Family

The function of KCT2 is not known. It was isolated from a library from human keratinocytes and is predicted to be a type I transmembrane protein .
Proline and serine-rich protein 3 (PROSER3)
Type: Family

The function of proline and serine-rich protein 3 (PROSER3) is not known.
HIRA-interacting protein 3 (HIRIP3)
Type: Family

HIRIP3 interacts with the HIRA histone chaperone . It can be phosphorylated by the serine-threonine kinase CK2 and may be involved in chromatin metabolism .
Uncharacterized protein C10orf62 (C10orf62)
Type: Family

The function of C10orf62 is not known.
60S ribosomal subunit assembly/export protein Loc1 (Loc1)
Type: Family

Loc1 is required for efficient assembly and nuclear export of the 60S ribosomal subunit . Budding yeast Loc1 recognizes double-stranded RNA structures and is required for efficient localization of ASH1 mRNA .
SWR1-complex protein 3 (Swc3)
Type: Family

Swc3 is a component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling . SWC3 has been used to refer to both SWC3/YAL011W, whose gene product is involved in chromatin remodeling and ER biogenesis, and ALR1/YOL130W, a plasma membrane transporter.
Mim2 (Mim2)
Type: Family

Mim2 is part of the Mim1/Mim2 complex, which is specific to fungi. This complex is responsible for the assembly and/or insertion of a subset of mitochondrial outer membrane proteins, including subunits of the main mitochondrial outer membrane translocase .
Cytochrome B pre-mRNA-processing protein 6 (Cbp6)
Type: Family

In Saccharomyces cerevisiae, Cbp6 is a mitochondrial protein and a cytochrome b translation regulator. It forms a complex with Cbp3; this complex is required for efficient synthesis of cytochrome b and for protection of the newly synthesized protein from proteolysis .

This entry also includes the Cbp6 homologue from Schizosaccharomyces pombe. In contrast to budding yeast, fission yeast Cbp6 is not required for the translation of mitochondrial mRNAs, but functions at a post-translational step of respiratory complex biogenesis .
Protein Big1 (Big1)
Type: Family

Protein Big1 is a putative endoplasmic reticulum membrane protein required for normal beta-1,6-glucan synthesis in yeast .
POU domain class 2-associating factor 2 (POU2AF2)
Type: Family

POU domain class 2-associating factor 2 (also known as Protein OCA-T1) is a transcriptional coactivator that specifically associates with POU2F3 , forming a complex that drives the development of tuft cells, a rare chemosensory cells that coordinate immune and neural functions within mucosal epithelial tissues .