SII-SWORD/CoKE huggingface dataset:
Transcription initiation factor TFIID subunit 12 (TAF12)
Type: Family

Transcription initiation factor TFIID subunit 12 (TAF12) is a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA , SALSA and SLIK .

The DNA-binding general transcription factor complex TFIID is central to the initiation of DNA-dependent RNA polymerase II transcription. TFIID is the only general transcription initiation factor that bind to the TATA box. The binding of TFIID to the TATA-box is the first step in the formation of a complex able to initiate transcription . TFIID consists of the TATA binding protein (TBP) and 14 TBP-associated factors (TAFs). One copy of each TAF1, TAF2, TAF3, TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, TAF9, TAF10, TAF12, and three copies of TAF14 .

The transcription regulatory histone acetylation complex Spt-Ada-Gcn5 acetyltransferase (SAGA) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. SAGA preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B . SAGA is known as PCAF in vertebrates and PCAF acetylates nucleosomal histone H3 . The SAGA complex consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1, and some of these components are present as two copies. The complex is built up from distinct modules, each of which has a separate function and crosslinks with either other proteins or other modules in the complex .

SLIK (SAGA-like) is a multi-subunit histone acetyltransferase complex that preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B. It is an embellishment of the SAGA complex. The yeast SLIK complex consists of at least TRA1, CHD1, SPT7, CC TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8 (a deubiquitinase), GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9 .

The yeast SALSA complex is an altered form of the SAGA complex and consists of at least TRA1, SPT7 (C-terminal truncated form), TAF5, ADA3, SPT20, TAF12, TAF6, HFI1, GCN5, ADA2 and SPT3 .
E3 ubiquitin-protein ligase HECW, C2 domain (C2_HECW)
Type: Domain

HECW1 (HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1), also known as NEDL1, is an HECT-type E3 ubiquitin protein ligase highly expressed in favorable neuroblastomas . NEDL1 is thought to normally function in the quality control of cellular proteins by eliminating misfolded proteins. This is thought to be accomplished via a mechanism analogous to that of ER-associated degradation by forming tight complexes and aggregating misfolded proteins that have escaped ubiquitin-mediated degradation . NEDL1 is thought to stimulate p53-mediated apoptosis .

NEDL1 shares large homology and structure with NEDL2, including a C2 domain at the N terminus, two WW domains in the middle of the protein, and a HECT domain at the C terminus . NEDL2 regulates the stability of p73 and functions as a regulator of the metaphase to anaphase transition .

This entry represents the C2 domain of NEDL1 and NEDL2.
Transcription initiation factor TFIID subunit 6 (TAF6)
Type: Family

Transcription initiation factor TFIID subunit 6 (TAF6) is a component of the DNA-binding general transcription factor complex TFIID and the regulatory transcription regulatory histone acetylation (HAT) complexes SAGA , SALSA and SLIK .

The DNA-binding general transcription factor complex TFIID is central to the initiation of DNA-dependent RNA polymerase II transcription. TFIID is the only general transcription initiation factor that bind to the TATA box. The binding of TFIID to the TATA-box is the first step in the formation of a complex able to initiate transcription . TFIID consists of the TATA binding protein (TBP) and 14 TBP-associated factors (TAFs). One copy of each TAF1, TAF2, TAF3, TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, TAF9, TAF10, TAF12, and three copies of TAF14 .

The transcription regulatory histone acetylation complex Spt-Ada-Gcn5 acetyltransferase (SAGA) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. SAGA preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B . SAGA is known as PCAF in vertebrates and PCAF acetylates nucleosomal histone H3 . The SAGA complex consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1, and some of these components are present as two copies. The complex is built up from distinct modules, each of which has a separate function and crosslinks with either other proteins or other modules in the complex .

SLIK (SAGA-like) is a multi-subunit histone acetyltransferase complex that preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B. It is an embellishment of the SAGA complex. The yeast SLIK complex consists of at least TRA1, CHD1, SPT7, CC TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8 (a deubiquitinase), GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9 .

The yeast SALSA complex is an altered form of the SAGA complex and consists of at least TRA1, SPT7 (C-terminal truncated form), TAF5, ADA3, SPT20, TAF12, TAF6, HFI1, GCN5, ADA2 and SPT3 .
FGD2, N-terminal PH domain (FGD2_PH1)
Type: Domain

In general, FGDs (including FGD1, FGD2, FGD3 and FGD4/Frabin) have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain . FGD2 is expressed by antigen-presenting cells where it may be involved in leukocyte signaling and vesicle trafficking .

This entry represents the N-terminal PH domain of FGD2.
Histone acetyltransferase GCN5 (GCN5)
Type: Family

This entry includes histone acetyltransferases GCN5, GCNE, KAT2A and KAT2B (all of which are included in

). GCN5 acetylates histones H2B, H3 and H4, providing a specific tag for epigenetic transcription activation. GCN5 is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA , SLIK , SALSA and ADA . GNCE acts as an acetyltransferase that acetylates histones H2B, H3 and H4, and contributes to H2A.Z acetylation. Also acts as a benzoyltransferase and benzoylates adhB at 'Lys-393' which activates adhB to affect the development, secondary metabolism, pathogenicity, and stress response .
Mammals have two paralogues: KAT2A (also known as GCN5) and KAT2B. KAT2A acetylates core histones to provide a specific tag for epigenetic transcription activation but not nucleosome core particles. It also acetylates proteins such as CEBPB . KAT2A is a component of the ATAC complex, which has acetyltransferase activity on histones H3 and H4 . KAT2B (also known as P300/calcium-binding protein (CBP)-associated factor or PCAF) can acetylate the core histones H3 and H4 as well as nucleosome core particles and non-histone proteins such as ACLY .

The transcription regulatory histone acetylation complex Spt-Ada-Gcn5 acetyltransferase (SAGA) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. SAGA preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B . SAGA is known as PCAF in vertebrates and PCAF acetylates nucleosomal histone H3 . The SAGA complex consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1, and some of these components are present as two copies. The complex is built up from distinct modules, each of which has a separate function and crosslinks with either other proteins or other modules in the complex .

SLIK (SAGA-like) is a multi-subunit histone acetyltransferase complex that preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B. It is an embellishment of the SAGA complex. The yeast SLIK complex consists of at least TRA1, CHD1, SPT7, CC TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8 (a deubiquitinase), GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9 .

The yeast SALSA complex is an altered form of the SAGA complex and consists of at least TRA1, SPT7 (C-terminal truncated form), TAF5, ADA3, SPT20, TAF12, TAF6, HFI1, GCN5, ADA2 and SPT3 .

The ADA complex is a transcription regulatory histone acetylation (HAT) complex. ADA preferentially acetylates nucleosomal histones H3 (at 'Lys-14' and 'Lys-18') and H2B. The complex consists of at least ADA2, ADA3, AHC1, and GCN5. AHC1 is required for the overall structural integrity of the ADA complex .
ARHGEF12, PH domain (ARHGEF12_PH)
Type: Domain

ARHGEF12 (also called LARG) is a Rho guanine-nucleotide exchange factor that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. LARG contains a regulator of G protein signaling (RGS) homology (RH) domain, the catalytic Dbl homology (DH) domain and the pleckstrin homology (PH) domain. The DH and PH domains bind RhoA and catalyze the exchange of GDP for GTP on RhoA. The active site of RhoA adopts two distinct GDP-excluding conformations among the four unique complexes in the asymmetric unit. The LARG PH domain also contains a potential protein-docking site. LARG forms a homotetramer via its DH domains .
SAGA-associated factor 29 (SGF29)
Type: Family

SAGA-associated factor 29 (SGF29) is a chromatin reader and a component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK . In the SAGA complex, SGF29 binds histone H3 that has been methylated at Lys-4 (H3K4me), and preferably binds the trimethylated form (H3K4me3) . SGF29 also acts as a boundary, preventing the spread of heterochromatin into neighbouring genes . SGF29 contains two Tudor domains.

The transcription regulatory histone acetylation complex Spt-Ada-Gcn5 acetyltransferase (SAGA) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. SAGA preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B . SAGA is known as PCAF in vertebrates and PCAF acetylates nucleosomal histone H3 . The SAGA complex consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1, and some of these components are present as two copies. The complex is built up from distinct modules, each of which has a separate function and crosslinks with either other proteins or other modules in the complex .

SLIK (SAGA-like) is a multi-subunit histone acetyltransferase complex that preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B. It is an embellishment of the SAGA complex. The yeast SLIK complex consists of at least TRA1, CHD1, SPT7, CC TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8 (a deubiquitinase), GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9 .
Rho guanine nucleotide exchange factor 11, PH domain (PRG_PH)
Type: Domain

Rho guanine nucleotide exchange factor 11, also known as PDZ-RhoGEF, is a guanine nucleotide exchange factor (GEFs) for Rho GTPase that plays critical roles in signalling . PDZ-RhoGEF uses its PDZ domains to bind class B plexins and plays a role in axon guidance . It is involved in neurotrophin-induced neurite outgrowth .

PDZ-RhoGEF contains an N-terminal PDZ domain, a regulators of G-protein signaling-like (RGSL) domain, a linker region, and C-terminal Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. This entry represents the PH domain .
SAGA-associated factor 73 (SGF73)
Type: Family

SAGA-associated factor 73 (SGF73) is a component of the transcription regulatory histone acetylation (HAT) complex SAGA .

The transcription regulatory histone acetylation complex Spt-Ada-Gcn5 acetyltransferase (SAGA) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. SAGA preferentially acetylates histones H3 and H2B and deubiquitinates histone H2B . SAGA is known as PCAF in vertebrates and PCAF acetylates nucleosomal histone H3 . The SAGA complex consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1, and some of these components are present as two copies. The complex is built up from distinct modules, each of which has a separate function and crosslinks with either other proteins or other modules in the complex .
Leukocyte surface antigen CD47, IgV (IgV_CD47)
Type: Domain

CD47 was originally identified as integrin-associated protein (IAP). It is a transmembrane glycoprotein that possesses an immunoglobulin variable (IgV) like N-terminal domain, five transmembrane domains and an alternatively spliced C terminus. It functions as a marker of self on erythrocytes, and likely also on other cells, by binding to the inhibitory receptor SIRPalpha . CD47-induces caspase-independent cell death may be mediated by cytoskeleton reorganisation . The protein can also act as a thrombospondin receptor .

This entry represents the IgV domain of of CD47. The interaction of CD47 with integrins is dependent on its IgV and transmembrane domains. The IgV domain and transmembrane domain of CD47 have also been found to be sufficient for the association with actin .
ARHGEF2, PH domain (ARHGEF2_PH)
Type: Domain

ARHGEF2, also called GEF-H1, acts as guanine nucleotide exchange factor (GEF) for RhoA GTPases . It is thought to play a role in actin cytoskeleton reorganization in different tissues since its activation induces formation of actin stress fibres. ARHGEF2 contains a C1 domain followed by Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA . This entry represents the PH domain of ARHGEF2.
Dedicator of cytokinesis C, C2 domain (C2_Dock-C)
Type: Domain

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).

This entry represents the C2 domain found in the Dock-C members. In addition to the C2 domain (also known as DHR-1 domain) and the DHR-2 domain, Dock-C members contain a functionally uncharacterised domain upstream of the C2 domain. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock1 (also known as Dock180) and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3) .
Dedicator of cytokinesis D, C2 domain (C2_Dock-D)
Type: Domain

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).

This entry represents the C2 domain of the Dock-D members. In addition to the C2 domain (also known as the DHR-1 domain) and the DHR-2, Dock-D members contain a functionally uncharacterised domain and a PH domain upstream of the C2 domain. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock1 (also known as Dock180) and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The PH domain broadly binds to phospholipids and is thought to be involved in targeting the plasma membrane .
PHLDB1/2/3, PH domain (PHLDB1/2/3_PH)
Type: Domain

PHLDB1, -2, and -3 (or LL5alpha, -beta, and -gamma) belong to the LL5 protein family. They contain a C-terminal PH domain. PHLDB3 is shorter and has no similarities with PHLDB1 and PHLDB2 in other regions, including the CLASP-binding region .
Dedicator of cytokinesis B, C2 domain (C2_Dock-B)
Type: Domain

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).

This entry represents the C2 domain of the Dock-B members. Most of these members have been shown to be GEFs specific for Rac, although Dock4 has also been shown to interact indirectly with the Ras family GTPase Rap1, probably through Rap regulatory proteins. In addition to the C2 domain (also known as DHR-1 domain) and the DHR-2 domain, Dock-B members contain a SH3 domain upstream of the C2 domain and a proline-rich region downstream. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock1 (also known as Dock180) and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3).
PLEKHM3, PH domain 1 (PLEKHM3_PH_1)
Type: Domain

PLEKHM3 (also called differentiation associated protein/DAPR) exists as three alternatively spliced isoforms that participate in metal ion binding. It contains 2 PH domains and 1 phorbol-ester/DAG-type zinc finger domain. PLEKHM3 is involved in skeletal muscle differentiation . This entry represents the first PH domain of PLEKHM3.
Transcription initiation factor TFIID subunit 2 (TAF2)
Type: Family

Transcription initiation factor TFIID subunit 2 (TAF2) is a component of the general purpose transcription factor complex TFIID . This entry includes TAF2 from animals, plants and fungi.

In yeast, TAF2 functions as a component of the DNA-binding general transcription factor complex TFIID. Its binding to a promoter, whether or not it contains a TATA element, represents the initial step in pre-initiation complex (PIC) formation. TAF2 plays a crucial role in regulating gene expression by RNA polymerase II through various mechanisms, including interaction with transcription activators, recognition and selectivity of core promoters, interactions with TFIIA and TFIIB, chromatin modification via histone acetylation by TAF1, facilitation of DNA unwinding, and initiation of transcription. In mammals, the TAF2 basal transcription factor complex plays a major role in the initiation of RNA polymerase II (Pol II)-dependent transcription . It recognises and binds to promoters with or without a TATA box via its TBP subunit (TATA-box-binding protein), promoting the assembly of the PIC . The complex comprises TBP and TBP-associated factors (TAFs), including TAF1, TAF2, TAF3, TAF4, TAF5, TAF6, TAF7, TAF8, TAF9, TAF10, TAF11, TAF12, and TAF13 . TAF2, in particular, forms a promoter DNA-binding subcomplex with TAF7 and TAF1 .

The DNA-binding general transcription factor complex TFIID is central to the initiation of DNA-dependent RNA polymerase II transcription. TFIID is the only general transcription initiation factor that bind to the TATA box. The binding of TFIID to the TATA-box is the first step in the formation of a complex able to initiate transcription . TFIID consists of the TATA binding protein (TBP) and 14 TBP-associated factors (TAFs). One copy of each TAF1, TAF2, TAF3, TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, TAF9, TAF10, TAF12, and three copies of TAF14 .
Cellobionic acid phosphorylase, N-terminal (GH94N_CBAP)
Type: Domain

Cellobionic acid phosphorylase (CBAP) is an intracellular enzyme from cellulolytic fungus and bacterium belonging to the glycoside hydrolase family 94 (GH94). It catalyzes the reversible phosphorolysis of cellobionic acid into glucose 1-phosphate and gluconic acid .

The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (

), cellodextrin phosphorylase (

), chitobiose phosphorylase ([ec:2.4.1.-]), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain - an (α/α)(6) barrel).
DOK4/5/6, PH domain (DOK4/5/6_PH)
Type: Domain

The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain binds to acidic phospholids and localizes proteins to the plasma membrane, while the PTB domain mediates protein-protein interactions by binding to phosphotyrosine-containing motifs .

This entry represents the PH domain found in Dok4, Dok5 and Dok6 .
Transcription initiation factor TFIID subunit 7 (TAF7)
Type: Family

Transcription initiation factor TFIID subunit 7 (TAF7) is a component of the general purpose transcription factor complex TFIID . This entry includes TAF7 from animals, plants and fungi.

The DNA-binding general transcription factor complex TFIID is central to the initiation of DNA-dependent RNA polymerase II transcription. TFIID is the only general transcription initiation factor that bind to the TATA box. The binding of TFIID to the TATA-box is the first step in the formation of a complex able to initiate transcription . TFIID consists of the TATA binding protein (TBP) and 14 TBP-associated factors (TAFs). One copy of each TAF1, TAF2, TAF3, TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, TAF9, TAF10, TAF12, and three copies of TAF14 .