SII-SWORD/CoKE huggingface dataset:
Type VI immunity for VRR-NUC (TsiV)
Type: Family

This entry represents bacterial immunity proteins that in are encoded by the PAAR2 cluster and have been named Type VI immunity for VRR-NUC (TsiV). These proteins form an effector-immunity pair with TseV (type VI effector VRR-NUC), the TseV-TsiV pair . These are α+β class of proteins whose surface is mainly electronegative with a a hydrophobic core formed by the N-terminal region .
Dedicator of cytokinesis C/D, N-terminal (DOCK_C/D_N)
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 N-terminal domain of the DOCK-C subfamily (DOCK 6, 7, 8) and DOCK-D subfamily (DOCK 9, 10, 11).
Protein of unknown function DUF3400 (DUF3400)
Type: Family

This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with

,

,

.
Signal-induced proliferation-associated 1-like protein, C-terminal (SIPA1L_C)
Type: Domain

This domain is found in C-terminal of the signal-induced proliferation-associated 1-like (SIPA1L) proteins, including SIPA1L 1-3 from humans. SIPA1Ls shares protein sequence similarity with signal-induced proliferation-associated protein 1 (SIPA1), which is a GTPase activator for the nuclear Ras-related regulatory proteins Rap1 and Rap2 . In rats SIPA1L1 (also known as SPAR) has been identified as a Rap-specific GTPase-activating protein .
Far11/STRP, C-terminal (Far11/STRP_C)
Type: Domain

This domain can be found in the C terminus of the yeast Far11 protein and the human STRP1/2 proteins.

Budding yeast Far11 interacts with the phosphatases Pph21, Pph22, and Pph3 and may be involved in the regulation of autophagy and the DNA damage signaling . STRP1/2 (also known as FAM40A/B) are regulators of cytoskeletal organization, cell morphology and migration .
S-locus receptor kinase, C-terminal (S-locus_recpt_kinase_C)
Type: Domain

This functionally uncharacterised domain of around 50 amino acids is found in the C terminus of S-locus receptor kinase proteins from plants .
Histidine kinase VxrA, sensor domain (VxrA_SD)
Type: Domain

This entry represents bacterial periplasmic sensor domains of histidine kinase VxrA and related proteins. VxrA is a component in two-component systems (TCSs) that sense fluctuating environmental conditions and elicit the appropriate cellular response. VxrA has a periplasmic sensor domain that is flanked by transmembrane helices and followed by a DHp (dimerization and histidine phosphotransfer) domain and a CA (catalytic ATP-binding) domain. The sensor domain has a complex α/β fold with unique topology .
Protein of unknown function DUF3405 (DUF3405)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 636 to 810 amino acids in length.
Protein of unknown function DUF3408 (DUF3408)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Capsid protein C, pestivirus (Capsid-C_pestivirus)
Type: Domain

This domain is found in the genome polyprotein from Pestivirus. This domain covers part of the capsid protein C region in the polyprotein.
Protein RETICULATA-related (RETICULATA-related)
Type: Family

This entry represents RETICULATA and related proteins from plants. Arabidopsis RETICULATA protein is involved in differential development of bundle sheath and mesophyll cell chloroplasts .
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain (PpnN_C)
Type: Domain

This entry represents a domain found at the C-terminal end of Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase from Escherichia coli (PpnN, also known as YgdH) and similar proteins mainly found in gammaproteobacteria. PpnN is a nucleosidase that catalyses the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates. This enzyme adopts a tetrameric configuration with allosteric (p)ppGpp binding sites located between subunits. The binding of this alarmone molecule, which play a role in the bacterial stringent response, gives rise to a large conformational change involving the terminal region that leads to the exposure of the catalytic pocket. The C-terminal domain shows a completely α-helical fold with an extension that wraps around the central domain .
Nucleoporin Nup186/Nup192/Nup205 (Nup186/Nup192/Nup205)
Type: Family

Proteins in this family are components of the nuclear pore complex (NPC). These protein are called nucleoporins (NUPs), which can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. This entry includes Nup186/Nup192/Nup205. In budding yeasts, Nup192 is located to the NPC core at the nuclear membrane and is essential for de novo assembly of NPCs . In humans, Nup205 forms a complex with NUP53, NUP93, NUP155 and lamin B .
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S (GlgE_dom_N/S)
Type: Domain

This entry represents domain N and S of GlgE.
Protein of unknown function DUF3419 (DUF3419)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 398 to 802 amino acids in length.
Protein of unknown function DUF3422 (DUF3422)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 426 to 444 amino acids in length.
ParD-like antitoxin of type II bacterial toxin-antitoxin system (ParD-like)
Type: Family

ParD-like antitoxin is a family of archaeal and bacterial proteins of a type II bacterial toxin-antitoxin system. Many of the cognate toxins for these molecules fall into family ParE-like_toxin,

. Gene-pairs are expressed from the same operon, the toxin of the pair being expressed first, eg, for

and

.
Ankyrin repeat domain-containing protein 13 (ANKRD13)
Type: Family

This entry represents ankyrin repeat domain-containing protein 13 (ANKRD13). At least 4 subtypes are known to exist, termed A-D. ANKRD13C has been experimentally characterised and acts as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2 . ANKRD13A/B/D are ubiquitin-binding proteins that specifically recognise and bind Lys-63-linked ubiquitin. They positively regulate the internalisation of ligand-activated EGFR by binding to the Ub moiety of ubiquitinated EGFR at the cell membrane .
Protein of unknown function DUF3425 (DUF3425)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 120 to 143 amino acids in length.
Protein of unknown function DUF3426 (DUF3426)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Protein of unknown function DUF3427 (DUF3427)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with

,

.
Protein of unknown function DUF3429 (DUF3429)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 147 to 245 amino acids in length.
Counting factor-associated protein A/B/C (CfaA/B/C)
Type: Family

Developing Dictyostelium (Slime mold) cells form large aggregation streams that break up into groups of cells. Each group then becomes a fruiting body. Cells sense if there are too many cells in a stream by sensing the concentration of counting factor (CF), a protein complex secreted by the aggregating cells . This entry includes counting factor-associated protein A/B/C from Slime mold.
Protein of unknown function DUF3431 (DUF3431)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 291 to 390 amino acids in length. This protein has a conserved NLRC sequence motif.
Early growth response protein 1, C-terminal (EGR1_C)
Type: Repeat

EGR1 is a transcriptional regulator that binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases .
Protein of unknown function DUF3433 (DUF3433)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 784 to 1240 amino acids in length.
Vacuolar protein 14, C-terminal Fig4-binding domain (VAC14_Fig4p-bd)
Type: Domain

Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes) . This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system .

This entry represents the C-terminal domain of Vac14, which binds to Fig4p.
Protein of unknown function DUF3435 (DUF3435)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to

suggesting it may be an integrase enzyme.
Proteasome activator complex subunit 4, C-terminal domain (PSME4_C)
Type: Domain

This domain is typically between 142 to 163 amino acids in length is found at the C terminus of activator complex subunit 4 (gene name PSME4, PA2000 or BLM10), a component of the 19S cap complex of the eukaryotic 26S proteasome. The tertiary structure of BLM10 from
Saccharomyces cerevisiae
has been solved, showing that the C terminus is important for helping to form the BLM10 cap that covers the entry pore of the proteasome, restricting access for potential substrates. The C-terminal residues bind in the pocket between proteasome subunits alpha5 and alpha6, in a similar site to where the C-termini of the ATPases of the 19S proteasomal cap also bind .
Integrating conjugative element protein, PFL4704 (Integr_conj_element_PFL4704)
Type: Family

Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition.
Protein of unknown function DUF3440 (DUF3440)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 53 to 190 amino acids in length. This domain is found associated with

. This domain has a conserved KND sequence motif.
NFACT protein, C-terminal (NFACT-C)
Type: Domain

This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain .
Protein of unknown function DUF3443 (DUF3443)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 400 to 434 amino acids in length. This protein has two conserved sequence motifs: NPV and DNNG.
Haem-dependent oxidative N-demethylase, alpha subunit-like (HODM_asu-like)
Type: Family

This entry represents a family of proteins predominantly found in fungi and bacteria, including the alpha subunit of an haem-dependent oxidative N-demethylase (HODM) from Pseudomonas mendocina (Pmen_3455,

). This protein, catalytically active, is responsible for haem, oxygen and NADPH-dependent dimethylamine (DMA) binding. It shows an N- and C-terminally extended PAS haem binding domain structurally similar to the to the Aer2 PAS domain, but lacks the core PAS-domain α-helix that forms the Aer2 haem pocket, and displays extended β-strands and a longer loop .
Early growth response, N-terminal (EGR_N)
Type: Domain

Proteins containing this domain include early growth response protein 1/2/3 (EGR1/2/3). EGR1 is a transcriptional regulator that binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases . EGR2,
also known as Krox20, is an E3 ligase that sumoylates its Nab coregulators .
Symplekin/Pta1 (Symplekin/Pta1)
Type: Family

Proteins in this entry include Symplekin from animals and Pta1 from yeasts.

Symplekin is a scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing .

Pta1 is involved in pre-tRNA processing. Pta1 is a subunit of the cleavage and polyadenylation factor (CPF), which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB .
Protein of unknown function DUF3455 (DUF3455)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 174 to 251 amino acids in length.
Domain of unknown function DUF3456 (DUF3456)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in a number of proteins, including protein canopy homologues and CRELD1 and 2.
Protein of unknown function DUF3460 (DUF3460)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
WASH1, WAHD domain (WASH1_WAHD)
Type: Domain

This entry represents the N-terminal WAHD domain (N-terminal WASH homology regions) of the WASH1 protein, which is a component of the WASH complex that is present at the surface of endosomes and activates the Arp2/3-mediated F-actin polymerisation . This domain covers the conserved WHD1/EVH1 and WHD2 domains. WASH1 interact with FAM21 via its WHD1 domain and binds to tubulin through its WHD2 domain .

The WASH complex consists of several subunits: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
PAM68-like (PAM68-like)
Type: Family

This entry includes chloroplastic protein PAM68 and some uncharacterised proteins from Cyanobacteria (blue-green algae). PAM68 is involved in early steps in photosystem II (PSII) biogenesis and in maturation and stability of newly synthesized psbA protein .
Protein of unknown function DUF3465 (DUF3465)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Protein of unknown function DUF3467 (DUF3467)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length.
Fungal transcription factor (Fun_TF)
Type: Family

Proteins in family are transcription factors typically found in fungi, including acriflavine sensitivity control protein , arginine metabolism regulation protein II , lysine biosynthesis regulatory protein LYS14 , and others . DibT is part of the gene cluster that mediates the biosynthesis of pestalotiollide B which is part of dibenzodioxocinones, a novel class of inhibitors against cholesterol ester transfer protein (CEPT).
XRN2-binding (XTBD) domain (XTBD)
Type: Domain

XRN2 is an essential eukaryotic exoribonuclease that processes and degrades various substrates. The ~80-residue XRN2-binding domain (XTBD) constitutes an XRN2-binding module that is employed by different metazoan proteins to link to XRN2 , such as:

Caenorhabditis elegans Partner of Xrn-Two protein 1, or PAXT-1 for short. Plays a role in maintenance of steady-state concentration and turnover of microRNAs (miRNA) by degradation of mature miRNA in complex with the exoribonuclease XRN-2 .

Mammalian CDKN2A-interacting protein (CDKN2AIP) or Collaborator of ARF (CARF) that regulates DNA damage response in a dose-dependent manner through a number of signaling pathways involved in cell proliferation, apoptosis .

Mammalian CDKN2AIP N-terminal-like protein (CDKN2AIPNL).

The XTBD domain folds into a globular four-helix bundle (H1-H4) connected by three loops (L1-L3). H1-H3 form an antiparallel helical array and H4 folds back on top of H2 and H3 at a 90degree angle. The four-helical bundle is mainly stabilized by hydrophobic helix-helix interactions together with additional polar interactions between side chains located on neighbouring helices. The four-helix bundle of XTBD represents a structurally unique arrangement for XRN2 binding .
Peptidase S12, Pab87-related, C-terminal (Peptidase_S12_Pab87-rel_C)
Type: Domain

This entry represents the C-terminal domain of a family of peptidases which belong to MEROPS peptidase family S12, clan SE. The structure of the Pyrococcus abyssi Pab87 peptidase has been determined at 2.2 A resolution . Pab87 is a self-compartmentalizing proteases that orchestrates protein turnover through an original architecture characterised by a central catalytic chamber.

Also containing this domain are the unguisins hydrolases (UngD). UngD catalyzes the hydrolysis (between the D-tryptophan and GABA residues) of the cyclic heptapeptides known as unguisins, yielding linear peptides
THO complex, subunit THOC1 (THO_THOC1)
Type: Family

THO complex subunit 1 (THOC1; its homologues from plants and yeast HPR1) is a component of the THO subcomplex of the TREX complex, which is involved in coupling mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX plays central roles during mRNP (messenger ribonucleoprotein) maturation and export from the nucleus to the cytoplasm . The THO complex is recruited to transcribed genes and moves along the gene with the elongating polymerase during transcription. THO is important for stabilizing nascent RNA in the RNA polymerase II elongation complex by preventing formation of DNA:RNA hybrids behind the elongating polymerase . In plants, HPR1 plays a role in disease resistance .
Protein of unknown function DUF3472 (DUF3472)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in pro and eukaryotes. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Fatty acid desaturase, N-terminal (FAS_N)
Type: Domain

This domain is found in fatty acid desaturases (FADs), mainly from plants and fungi.
Domain of unknown function DUF3475 (DUF3475)
Type: Domain

This entry represents the N-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with DUF668 (

).

PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth .
Peptidase G2, IMC autoproteolytic cleavage domain (Peptidase_G2)
Type: Domain

This domain is found at the very C terminus of bacteriophage parallel β-helical tailspike proteins. It carries the enzymic residues that induce autoproteolytic cleavage to bring about maturation of the folding process of the helix in a chaperone-like manner. The domain thus mediates the assembly of a large tailspike protein and then releases itself after maturation. These C-terminal regions that autoproteolytically release themselves after maturation are exchangeable between functionally unrelated N-terminal proteins and have been identified in a number of bacteriophage tailspike proteins .
SpoIIAA-like (SpoIIAA-like)
Type: Family

These proteins adopt an α/β SpoIIAA-like fold, similar to that found in STAT

. They adopt open and closed conformations arising from different arrangements of their α2 and α3 helices. They may be membrane associated and may function as carriers of non-polar compounds .
S-adenosylmethionine-dependent methyltransferase Bmt2-like (Bmt2/SAMTOR)
Type: Family

This entry includes Bmt2 from yeasts and SAMTOR from animals. They contain a class I Rossmann fold methyltransferase domain.

In Saccharomyces cerevisiae, Bmt2 is a nucleolar S-adenosylmethionine-dependent rRNA methyltransferase that is responsible for the N-1-methyl-adenosine base modification of 25S rRNA . It specifically methylates the N1 position of adenine 2142 in 25S rRNA .
Alpha-2-macroglobulin MG3 domain (Alpha_2_Macroglob_MG3)
Type: Domain

This is the N-terminal MG3 domain from alpha-2-macroglobulin .
Ribonuclease Zc3h12a-like, NYN domain (RNase_Zc3h12_NYN)
Type: Domain

This domain is found in the Zc3h12a protein and NEDD4-binding protein 1 (N4BP1). Zc3h12a has been shown to be a ribonuclease that controls the stability of a set of inflammatory genes . This domain belongs to the PIN domain superfamily and it has also been identified as part of the NYN domain family .

N4BP1 is a potent suppressor of cytokine production that acts as a regulator of innate immune signalling and inflammation . It acts as a restriction factor against some viruses, such as HIV-1. N4BP1 restricts HIV-1 replication by binding to HIV-1 mRNAs and mediating their degradation via its ribonuclease activity .
Major vault protein, shoulder domain (MVP_shoulder)
Type: Domain

The major vault protein is the major polypeptide component of a large cellular ribonuclear protein complex found in the cytoplasm of eukaryotic cells. Several roles for vaults have been proposed. Vault proteins have been associated with development of multi-drug resistance . They have also being implicated in the regulation of several cellular processes including transport mechanisms, signal transmission and immune responses .

This domain is found in the Major Vault Protein and has been called the shoulder domain . This family includes two bacterial proteins

and

. This suggests that some bacteria may possess vault particles.
Protein of unknown function DUF3482 (DUF3482)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 289 to 301 amino acids in length. This domain is found associated with

.