SII-SWORD/CoKE huggingface dataset:
Peptidase C39-like (Peptidase_C39-like)
Type: Domain

This entry represents a group of peptidase C39-like proteins.

The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are lacking the nucleotide-binding transporter signature or have different domain architectures .
Outer membrane lipoprotein BamD-like (BamD-like)
Type: Domain

BamD, also called YfiO, is part of the β-barrel assembly machinery (BAM), which is essential for the folding and insertion of outer membrane proteins (OMPs) in the OM of Gram-negative bacteria. Transmembrane OMPs carry out important functions including nutrient and waste management, cell adhesion, and structural roles. The BAM complex is composed of the β-barrel OMP BamA (also called Omp85/YaeT) and four lipoproteins BamBCDE. BamD is the only BAM lipoprotein required for viability. Both BamA and BamD are broadly distributed in Gram-negative bacteria, and may constitute the core of the BAM complex. BamD contains five tetratricopeptide repeats (TPRs). The three TPRs at the N terminus may participate in interaction with substrates, while the two TPRs in the C terminus may be involved in binding with other BAM components .
Conserved virulence factor B, first S1 domain (CvfB_S1_st)
Type: Domain

This entry represents the first S1 domain found at the N-terminal of conserved virulence factor B proteins. The S1 domain has an OB-fold structure and is involved in nucleic acid binding.

Conserved virulence factor B proteins contribute to the expression of virulence factors and to pathogenicity via both agr-dependent and agr-independent pathways .
Glycine zipper domain (Gly-zipper)
Type: Domain

This entry represents a glycine zipper domain.
Peptidase MA-like domain (Peptidase_MA-like_dom)
Type: Domain

This entry represents a domain found in a group of putative bacterial peptidases belonging to the MA clan.

Clan MA is one of two zinc-dependent metallopeptidases that contain the HEXXH motif. The two histidines are zinc ligands. The structures of this clan show the active site is between its two sub-domains.
FAS1-like, dehydratase domain region (FAS1-like_DH_region)
Type: Domain

This entry represents a region of the dehydratase domain found in Fatty acid synthase subunit beta from Saccharomyces cerevisiae (FAS1, ) and similar sequences predominantly found in eukaryotes and bacteria. FAS1 catalyses the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. This entry is often found associated to

.
AmiC, periplasmic binding domain (AmiC_PBP1)
Type: Domain

This entry includes the periplasmic binding domain of aliphatic amidase expression-regulating protein (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon are induced .
RNF126, RING finger, H2 subclass (RNF126_RING-H2)
Type: Domain

RNF126 is a Bag6-dependent E3 ubiquitin ligase that is involved in the mislocalized protein (MLP) pathway of quality control . It regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR) . Moreover, RNF126 promotes cancer cell proliferation by targeting the tumour suppressor p21 for ubiquitin-mediated degradation, and could be a novel therapeutic target in breast and prostate cancers . It is also able to ubiquitinate cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification . In addition, RNF126 and the related protein, RNF115 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitination of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors . RNF126 contains an N-terminal BCA2 zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger.

This entry represents the C3H2C3-type RING-H2 finger.
NS2A-like (NS2A-like)
Type: Domain

This domain can be found in NS2A from Coronavirus and protein VP3 from Rotavirus A. This domain has a phosphoesterase module (2H) that could function in capping and processing of viral RNAs .
Opioid growth factor receptor (OGFr)
Type: Family

Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The opioid growth factor receptor is an integral membrane protein associated with the nucleus .
Prolyl 3-hydroxylase (P3H)
Type: Family

This entry represents prolyl 3-hydroxylase, including prolyl 3-hydroxylase catalyses 1-3 (P3H1-3) from humans. P3H1, also known as leprecan-1, is responsible for converting proline to 3-hydroxyproline (3Hyp) in type I collagen. P3H2 is responsible for 3-hydroxylating multiple proline sites in collagen types I, II, IV, and V . However, P3H3 is not required for normal prolyl 3-hydroxylation on collagen chains .
Amyloid beta precursor protein binding family B member 1/2/3 (APBB1/2/3)
Type: Family

This entry represents the FE65 family, whose members include FE65 (APBB1), FE65L1 (APBB2), and FE65L2 (APBB3). They are adaptor proteins that bind the C-terminal region of the amyloid precursor protein (APP) .

APBB1 is a neuronal adaptor protein involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP . It contains three protein-protein interaction domains, one WW domain, and two phosphotyrosine-binding domains (PTBs). The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD) including the GYENPTY internalization sequence fingerprint .

This entry also includes an Fe65 homologue from C. elegans, Feh-1. Besides binding to amyloid precursor protein, it is also involved in the same pathway that controls nematode pharyngeal pumping .
E3 ubiquitin-protein ligase Rad18 (Rad18)
Type: Family

This entry includes Rad18 from eukaryotes. Rad18 is a E3 ubiquitin ligase required for postreplication repair . In budding yeast, Rad18 forms a heterodimer with Rad6 to monoubiquitinate PCNA at a highly conserved lysine, 'Lys-164' . In humans, Rad18 associates to the E2 ubiquitin conjugating enzyme UBE2B to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on 'Lys-164' .
Oncostatin-M (OSM)
Type: Family

Oncostatin-M is a cytokine produced by activated lymphoid cells that regulates the proliferation of a number of tumour cell lines. It may play a role in the pathogenesis of AIDS-KS .
Arginine vasopressin-induced protein 1 (AVPI1)
Type: Family

Arginine vasopressin-induced protein 1, also known as VIP32, may be involved in MAP kinase activation, epithelial sodium channel (ENaC) down-regulation and cell cycling .
Transcriptional and immune response regulator (Tcim)
Type: Family

Transcriptional and immune response regulator (Tcim; also known as C8orf4 or TC1) is a regulator implicated in cancer and inflammation . It is highly expressed in several tumours and implicated in tumorigenesis. It plays a role in the mitogen-activated MAPK2/3 signaling pathway, and positively regulates G1-to-S-phase transition of the cell cycle . It negatively regulates the self-renewal of liver cancer stem cells via suppression of NOTCH2 signalling .
Fibronectin type III domain-containing protein 11 (FNDC11)
Type: Family

The function of FNDC11 is not clear.
Thiamine-triphosphatase (THTPA)
Type: Family

Thiamine-triphosphatase is a hydrolase highly specific for thiamine triphosphate (ThTP) . It belongs to the CYTH superfamily .
Transcription factor-like 5/SOLH1/2 (TCFL5/SOLH1/2)
Type: Family

This family includes a group of mammalian proteins involved in germline differentiation, including TCFL5, Spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein 1/2 (SOLH1/2). TCFL5 is a transcription factor that interacts with the Calmegin gene promoter in mouse spermatogenesis . SOLH1/2 are transcription regulators of both male and female germline differentiation. They suppress genes involved in spermatogonial stem cells maintenance, and induces genes important for spermatogonial differentiation. They also coordinates oocyte differentiation without affecting meiosis I .
Heat shock factor 2-binding protein (HSF2BP)
Type: Family

Heat shock factor 2-binding protein (HSF2BP) may be involved in modulating HSF2 activation in testis . It may play a role in regulating BNC1 (a zinc finger transcriptional factor) activity and subcellular localization during spermatogenesis .
SERTA domain-containing protein 3 (SERTAD3)
Type: Family

SERTAD3, also known as RBT1, is a transcriptional co-activator that binds the second subunit of replication protein A .
Cilia- and flagella-associated protein 46 (CFAP46)
Type: Family

CFAP46 is a part of the central apparatus of the cilium axoneme and plays a role in cilium movement and thereby cell motility .
TMEM248/TMEM219 domain (TMEM248/TMEM219_dom)
Type: Domain

Proteins containing this domain include TMEM248 and TMEM219 (also known as insulin-like growth factor-binding protein 3 receptor, IGFBP-3R) from animals. TMEM219 is a cell death receptor and is essential for the IGFBP-3-induced apoptosis and tumor suppression . The function of TMEM248 is not clear.
F-box only protein 4 (FBXO4)
Type: Family

F-box only protein 4 (FBXO4) is a substrate-specific adaptor of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins .
TBCC domain-containing protein 1 (TBCC1)
Type: Family

TBCC-domain containing 1 (TBCCD1) has a role in internal cell organization in animals, Chlamydomonas reinhardtii, and trypanosomes . In humans, it is required for centrosome and Golgi apparatus positioning .
Developmental pluripotency-associated protein 2/4 (Dppa2/4)
Type: Family

Developmental pluripotency-associated protein 2 (Dppa2, also known as ECAT15-2) and Dppa4 (also known as ECAT15-1) have a common DNA binding domain known as the SAP motif. Dppa2 has been found to bind to the regulatory region of Nkx2-5 in embryonic stem (ES) cells . Dppa4 has been found to bind to both DNA and histone H3 necessary for the chromatin structure resistance to MNase and for the proper localization of Dppa4 in ES cell nuclei .
AP-5 complex subunit mu-1 (AP5M1)
Type: Family

AP5M1, also known as MUDENG, is part of AP-5, a probable fifth adaptor protein complex that may be involved in endosomal transport . AP5M1 is involved in cell death signaling .
F-box only protein 34/46 (FBXO34/46)
Type: Family

The functions of F-box only proteins 34 and 46 is not known. Homologues are found in vertebrates.
TE2IP/Rap1 (TE2IP/Rap1)
Type: Family

This entry includes fission yeast Rap1 and its homologue, TERF2IP (telomeric repeat-binding factor 2-interacting protein 1) from animals.

TERF2IP is a telomere-interacting protein that plays a role in protecting telomeres from initiating homology directed repair (HDR) . It is recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. It can also be recruited to extratelomeric 5'-TTAGGG-3' sites and regulates gene expression .

In Schizosaccharomyces pombe, Rap1 is involved in the regulation of telomere length and telomere position effect (TPE) . It is also involved in chromosomal bouquet formation .
Growth arrest-specific protein 1 (GAS1)
Type: Family

Growth arrest-specific protein 1 (GAS1) is a glycosylphosphatidylinositol-anchored protein involved in growth suppression . It inhibits cell proliferation when overexpressed in normal and transformed cell lines, and reduces tumour cell growth . It also promotes apoptosis , plays a role in mouse embryonic development , and suppresses melanoma metastases .
Myosin phosphatase-RhoA interacting protein, PH domain (M-RIP_PH)
Type: Domain

Myosin phosphatase-RhoA interacting protein (M-RIP) is proposed to play a role in myosin phosphatase regulation by RhoA. M-RIP contains two PH domains followed by a Rho binding domain (Rho-BD), and a C-terminal myosin binding subunit (MBS) binding domain (MBS-BD). The amino terminus of M-RIP with its adjacent PH domains and polyproline motifs mediates binding to both actin and Galpha. M-RIP brings RhoA and MBS into close proximity where M-RIP can target RhoA to the myosin phosphatase complex to regulate the myosin phosphorylation state. M-RIP does this via its C-terminal coiled-coil domain which interacts with the MBS leucine zipper domain of myosin phosphatase, while its Rho-BD, directly binds RhoA in a nucleotide-independent manner .

PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner . They share little sequence conservation, but all have a common fold, which is electrostatically polarised. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity . PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane . A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signalling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes .
HMG domain-containing protein 3 (HMGXB3)
Type: Family

HMGXB3 (HMG-box containing 3) belongs to the High Mobility Group superfamily, and participates in a range of cellular processes including cell migration and proliferation .
RNA-binding protein 48 (RBM48)
Type: Family

The function of RBM48 is not clear. It has been identified as a candidate gene for renal ciliopathies .
TANGO6/Rtp1 (TANGO6/Rtp1)
Type: Family

This entry includes Rtp1 from yeasts and TANGO6 from animals. Rtp1 is required for RNA polymerase II biogenesis . TANGO6 may be involved in protein secretion and Golgi organization .
RNA polymerase I-specific transcription initiation factor Rrn5 (Rrn5)
Type: Family

This entry represents Rrn5 from fungi. Rrn5 is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex .
Transcriptional regulatory protein Rxt2 (Rxt2)
Type: Family

Rxt2 is a component of the Rpd3 histone deacetylase complex (HDAC). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression and developmental events .
Small ribosomal subunit protein mS41 (Ribosomal_mS41)
Type: Family

The entry includes the mitochondrial small ribosomal protein mS41 family in fungi (previously known as Fyv4), a component of the mitochondrial ribosome small subunit . It is required for survival upon exposure to K1 killer toxin and has also been described in telomere length regulation .
Nuclear segregation protein Bfr1 (Bfr1)
Type: Family

This entry includes Bfr1 and related proteins, including C458.02c from the fission yeast Schizosaccharomyces pombe. Bfr1 is implicated in secretion and nuclear segregation in Saccharomyces cerevisiae .
AT-hook motif nuclear-localized protein (AHL)
Type: Family

This entry includes AT-hook motif nuclear-localized protein 1-14 (AHL1-14) from Arabidopsis. They have two conserved structural units, the AT-hook motif and the Plant and Prokaryote Conserved (PPC) domain, the latter also known as DUF296. Members of the AHL family regulate diverse aspects of growth and development in plants . AHL1 is a transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) .
Phytol/farnesol kinase (Phytol/farnesol_kinase)
Type: Family

This entry includes a group of kinases from plants and bacteria, including phytol kinase l and farnesol kinase from Arabidopsis.
VQ motif-containing protein 8/17/18/20/21/25 (VQ_8/17/18/20/21/25)
Type: Family

This entry includes a group of VQ motif-containing proteins from plants, including MKS1 (VQ21, At3g18690) and VQ8/17/18/20/25 from Arabidopsis.

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
VQ motif-containing protein 1/10 (VQ_1/10)
Type: Family

This entry includes a group of VQ motif-containing proteins from plants, including VQ1/10 from Arabidopsis.

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
VQ motif-containing protein 15/22 (VQ_15/22)
Type: Family

This entry includes a group of VQ motif-containing proteins from plants, including VQ15/22 from Arabidopsis. VQ15, also known as calmodulin-binding protein 25, can work as a negative regulator of osmotic stress tolerance .

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
VQ motif-containing protein 29 (VQ29)
Type: Family

This entry includes a group of VQ motif-containing proteins from plants, including VQ29 from Arabidopsis.

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
VQ motif-containing protein 4/11/13/19/31/33 (VQ_4/11/13/19/31/33)
Type: Family

This entry includes a group of VQ motif-containing proteins (VQPs) from plants, including VQ4/11/13/19/31/33 from Arabidopsis. This subgroup of VQPs can be phosphorylated by the MAPKs MPK3 and MPK6, and have been named MPK3/6-targeted VQPs (MVQs). VQ4, also known as MVQ1, may act as an inhibitor of WRKY functions .

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
VQ motif-containing protein 5/9/14 (VQ_5/9/14)
Type: Family

This entry includes a group of VQ motif-containing proteins from plants, including VQ5/9/14 from Arabidopsis. VQ14, also known as HAIKU1, regulates endosperm growth and seed size in Arabidopsis .

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
Protein SPIRAL1-like (SPR1/2/3/4/5)
Type: Family

This entry represents a group of plant proteins, including SPR1 and SP1L1-5 from Arabidopsis. They may share the same functions and act redundantly to control directional cell expansion by organizing cortical microtubule orientation .
Protein PLASTID MOVEMENT IMPAIRED 1-like (PMI1-like)
Type: Family

This entry represents a group of plant proteins, including protein PLASTID MOVEMENT IMPAIRED 1 (PMI1) and PMIR1/2 from Arabidopsis. PMI1 and PMIR1 are required for efficient chloroplast photorelocation movement . PMI1 is a mobile signal that initiates coordinated changes in protein-protein and protein-plasma membrane interactions for chloroplast movement in response to light, which determines where in the cell chloroplasts are able to anchor to the plasma membrane . PMIR2 seems not necessary for chloroplast and nuclear photorelocation movements . PMI1 has been found to mediate ABA sensitivity during germination .
Protein PHYTOCHROME KINASE SUBSTRATE (PKS)
Type: Family

This entry represents a group of plant proteins, including protein PHYTOCHROME KINASE SUBSTRATES 1-4 (PKS1-4) from Arabidopsis. PKS1 is a novel phot1 signaling element during phototropism, while PKS2 is a phototropin signaling element that regulates leaf flattening and leaf positioning . PKS4 modulates phytochrome-mediated control of hypocotyl growth orientation .