SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF5785 (DUF5785)
Type: Family

This is a family of proteins of unknown function predominantly found in Halobacteria.
PhoD-like phosphatase (PhoD_2-like)
Type: Domain

This entry represents a domain found in a group of predicted phosphatases based on their similarity to the bacterial PhoD phosphatases.
Protein of unknown function DUF5771 (DUF5771)
Type: Family

This is a family of uncharacterised proteins. Some members contain the GNAT domain and may have N-acetyltransferase activity.
Gfo/Idh/MocA-like oxidoreductase, bacterial type, C-terminal (Gfo/Idh/MocA_OxRdtase_bact_C)
Type: Domain

This entry represents a domain found in a group of predicted bacterial oxidoreductases. Proteins containing this domain are related to the GFO/IDH/MOCA family members that function as NAD(P)-dependent oxidoreductases. This domain is a α/β-domain that contributes to the substrate binding and catalysis .
Protein of unknown function DUF5770 (DUF5770)
Type: Family

This is a family of uncharacterised proteins found in Iridoviridae, including the uncharacterised protein 045L from frog virus 3.
Protein of unknown function DUF5769 (DUF5769)
Type: Family

This is a family of uncharacterised proteins found in Mimiviridae.
Protein of unknown function DUF5768 (DUF5768)
Type: Family

This is a family of uncharacterised proteins found in Pandoravirus.
Protein of unknown function DUF5767 (DUF5767)
Type: Family

The function of DUF5767 is not clear.
Protein of unknown function DUF5766 (DUF5766)
Type: Family

This is a family of uncharacterised proteins found in Pimascovirales.
Protein of unknown function DUF5765 (DUF5765)
Type: Family

The function of DUF5765 is not clear.
Protein of unknown function DUF5764 (DUF5764)
Type: Family

The function of DUF5764 is not clear.
Protein of unknown function DUF5763 (DUF5763)
Type: Family

The function of DUF5763 is not clear.
Minor capsid protein P9 transmembrane helices (P9_TM)
Type: Domain

This entry, previously known as DUF5762, represents the N-terminal transmembrane helices of the minor capsid protein P9 found in PBCV-1 and related viruses. These transmembrane helices are inserted in the bilayer membrane of the virus vesicle structure . P9 plays a role in the stabilisation of the capsomers .
Minor capsid protein P8, central region (P8_CR)
Type: Domain

This entry, previously known as DUF5761, represents the central region of the minor capsid protein P8 found in PBCV-1 and related viruses. The central region of P8 folds into a wedge-shaped structure that consists of three short α-helices wrapped around a long α-helix . P8 and other minor capsid proteins contribute to the stability of the pentasymmetrons of the viral capsid .
Domain of unknown function DUF5753 (DUF5753)
Type: Domain

This entry represents a putative ligand binding domain found in bacterial transcription regulators that have an N-terminal HTH domain.
Protein of unknown function DUF5760 (DUF5760)
Type: Family

The function of DUF5760 is not clear.
Protein of unknown function DUF5758 (DUF5758)
Type: Family

This is a family of uncharacterised proteins found in viruses and bacteria. Some members contain the pentapeptide repeat.
Protein of unknown function DUF5757 (DUF5757)
Type: Family

This is a family of uncharacterised proteins found in viruses. This entry includes virion structural protein ORF43 from Trichoplusia ni ascovirus 2c, ORF84 from Spodoptera frugiperda ascovirus 1a and ORF146 from Heliothis virescens ascovirus 3e. ORF43 has 32% amino acid identity to the predicted dynein-like beta-chain protein in SfAV-1a (ORF84) and HvAV-3e (ORF146) .
Protein of unknown function DUF5772 (DUF5772)
Type: Family

The function of DUF5772 is not clear.
Protein of unknown function DUF5773 (DUF5773)
Type: Family

This is a family of uncharacterised proteins found in Phycodnaviridae.
Protein of unknown function DUF5774 (DUF5774)
Type: Family

This is a groupof uncharacterised proteins found in Pimascovirales.
Protein of unknown function DUF5775 (DUF5775)
Type: Family

This is a family of uncharacterised proteins mostly found in phycodnaviruses. These proteins contain a predicted N-terminal transmembrane helix.
ABC transporter family G domain (ABCG_dom)
Type: Domain

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily which uses the hydrolysis of ATP to energise diverse biological import and export systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein (mostly in eukaryotes and bacterial exporters) or on two different ones (mostly bacterial importers) . The function of the integral inner-membrane protein is to translocate the substrate across the membrane and seems to play an important role in substrate recognition .

ABC family G is a multidrug ATP-binding cassette transporter expressed in the plasma membranes of several tissues that is involved in endogenous substrates translocation, modifies drug pharmacokinetics and acts as a protector against xenobiotics .

This domain is found in several ATP binding cassette transporters family G (ABCG).
Protein of unknown function DUF5778 (DUF5778)
Type: Family

DUF5778 proteins are predominantly found in Halobacteria.
DVNP family (DNVP)
Type: Family

DVNPs (dinoflagellate-viral-nucleoproteins) are a group of viral-derived proteins found in dinoflagellates. It has been hypothesized that DVNPs could have been transferred from viruses to dinoflagellate progenitors with canonical chromatin and eventually replaced the majority of histones as chromatin packaging proteins . This entry includes dinoflagellate viral nucleoprotein 5 (DNVP5) and related proteins.
Protein of unknown function DUF5755 (DUF5755)
Type: Family

This entry represents a family of uncharacterised proteins mainly found in Mimiviridae and Phycodnaviridae.
Protein of unknown function DUF5754 (DUF5754)
Type: Family

The function of DUF5754 is not clear.
Protein of unknown function DUF5779 (DUF5779)
Type: Family

DUF5779 proteins are predominantly found in Halobacteria.
SidE, DUB domain (SidE_DUB)
Type: Domain

This entry represents the N-terminal deubiquitinating (DUB) domain of SidE from Legionella pneumophila subsp. pneumophila .

The SidE family includes four large proteins SidE, SdeA, SdeB, and SdeC, required for efficient intracellular bacterial replication and catalyses ubiquitination in an E1/E2-independent manner. These proteins contain four domains: a DUB domain, a phosphodiesterase (PDE) domain, a mono-ADP-ribosyltransferase (mART) domain, and a coiled-coil (CC) domain .

Ubiquitination is a post-translational modification that regulates many cellular processes, the conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein . SidE family proteins can catalyse the non-canonical ubiquitination of several different substrate proteins, including Rab small GTPases, Reticulon-4 (Rtn4), and Rag small GTPases, as well as SidE proteins themselves . This specificity resides on the specific ubiquitin-binding surfaces of mART and the unique features of the PDE domain .

The DUB activity of SdeA is important for regulating the dynamics of ubiquitin association with the bacterial phagosome, but is not necessary for its role in intracellular bacterial replication .
SidE, mono-ADP-ribosyltransferase domain (SidE_mART)
Type: Domain

This entry represents the mono-ADP-ribosyltransferase (mART) domain that mediates the mono-ADP-ribosylation of ubiquitin, which is then transferred to serine residues of host proteins .

The SidE family includes four large proteins SidE, SdeA, SdeB, and SdeC, required for efficient intracellular bacterial replication and catalyses ubiquitination in an E1/E2-independent manner. These proteins contain four domains: a DUB domain, a phosphodiesterase (PDE) domain, a mono-ADP-ribosyltransferase (mART) domain, and a coiled-coil (CC) domain .

Ubiquitination is a post-translational modification that regulates many cellular processes, the conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein . SidE family proteins can catalyse the non-canonical ubiquitination of several different substrate proteins, including Rab small GTPases, Reticulon-4 (Rtn4), and Rag small GTPases, as well as SidE proteins themselves . This specificity resides on the specific ubiquitin-binding surfaces of mART and the unique features of the PDE domain .

The DUB activity of SdeA is important for regulating the dynamics of ubiquitin association with the bacterial phagosome, but is not necessary for its role in intracellular bacterial replication .
HOOK, N-terminal (HOOK_N)
Type: Domain

The Hook family consists of several proteins from different eukaryotic organisms, first identified in Drosophila melanogaster in which play a role in endocytic cargo sorting . In Drosophila and fungi there is a single Hook gene, whereas mammals have three Hook genes, Hook1, Hook2 and Hook3. Endogenous Hook3 binds to Golgi membranes while both Hook1 and Hook2 are localised to discrete but unidentified cellular structures . In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubule structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head .

They are a widely expressed class of dynein-associated cargo adaptor proteins which include different domains. The N-terminal part of these proteins is sufficient to form a stable complex with dynein-dynactin and includes the most conserved region within the first 160 amino acids, termed the Hook domain. This domain is followed by three coiled-coil domains, important for dimerization and activation of dynein-dynactin complex motility, and then a C-terminal domain that binds a variety of proteins specific for each Hook isoform, involved in binding to specific organelles (organelle-binding domains). All mammalian Hook isoforms form a complex with Fused Toes and the Fused Toes- and Hook-interacting protein; fungal homologues of these proteins are important for dynein-mediated early endosome transport by linking Hook to the cargo .

This entry includes residues in the first 160 amino acids at the N-terminal of Hook, which is the most conserved region and necessary for dynein-dynactin interaction. It interacts with dynein light intermediate chain 1 (LIC1) . This domain is also found in protein Daple and Girdin which are G-protein modulators involved in ciliogenesis and cilium morphology, integrity of the actin cytoskeleton, formation of actin stress fibres and lamellipodia and membrane sorting in the early endosome.
Golgin subfamily A , C-terminal binding motif (GOLGA_C)
Type: Conserved_site

This entry represents the C-terminal motif of the golgin subfamily A member 2 protein (or GM130) that is bound by the GRASP65 PDZ1 and PDZ2 domains . These interactions are required for their association and localisation of GRASP65 to the cis-cisternae.

Members of the Golgin subfamily A were identified as Golgi auto-antigens . They might be involved in maintaining cis-Golgi structure . One of the members of this family, member 2 or GM130, is a specific interacting partner of the small GTPase Rab1b and plays a key role in the disassembly and reassembly of the Golgi apparatus during mitosis. GM130 is also involved in vesicle tethering and fusion at the cis-cisternae to facilitate transit between transport vesicles and the stacked cisternae. It interacts with GRASPs proteins, which mediate the stacking of Golgi cisternae . Additionally, GM130 was localised to the spindle poles and regulates microtubule organisation . Structurally, GM130 is comprised of six coiled-coil regions in the middle, a Golgi-targeting domain at the C-terminal, and a p115-interacting motif at the N-terminal .
Ligase-CoA domain (Ligase_CoA_dom)
Type: Domain

Acetyl coenzyme A (acetyl-CoA) synthetases (ACDs) were first described in Pyrococcus furiosus and then in other Archaea members as the major energy-conserving enzymes. They catalyse the reversible formation of acetate and ATP from acetyl-CoA by using ADP and phosphate and are able to use other substrates such as phenylacetyl-CoA, indoleacetyl-CoA and isobutyryl-CoA, but not succinyl-CoA. They are involved in the conversion of acetyl-CoA to acetate and in the degradation of branched-chain amino acids via branched-chain-acyl-CoA esters. There are two isoforms ACD I and II which are heterotetramers (alpha2beta2) consisting of two different subunits, alpha and beta . Each ACD is composed of at least five subdomains with variable sequential arrangement, termed "domain shuffling", which confers a very diverse pattern of subdomain organisation within members of the ACD family.

This entry represents the C-terminal domain of the Acetate--CoA ligase [ADP-forming] subunit alpha which corresponds to the ligase CoA domain and adopts a flavodoxin fold .
Domain of unknown function DUF5780 (DUF5780)
Type: Domain

This domain adopts a Greek-key β sandwich topology, with long loops in some of the members. While a structure is known, the function of this domain is yet to be determined.
Protein of unknown function DUF5781 (DUF5781)
Type: Family

Proteins in this entry are predominantly found in Halobacteria.
EMC6-arch (EMC6-arch)
Type: Family

This family represents the ER membrane protein complex subunit 6 (EMC6) homologue from archaea. They contain three transmembrane regions.
Protein of unknown function DUF5783 (DUF5783)
Type: Family

Proteins in this entry are predominantly found in Halobacteria.
Protein of unknown function DUF5784 (DUF5784)
Type: Family

Proteins in this entry are predominantly found in Halobacteria.
Snu56-like U1 small nuclear ribonucleoprotein component (Snu56_snRNP)
Type: Family

This family is a component of the U1 snRNP particle, which recognises and binds the 5'-splice site of pre-mRNA. Together with other non-snRNP factors, U1 snRNP forms the spliceosomal commitment complex, which targets pre-mRNA to the splicing pathway .
Domain of unknown function DUF5746 (DUF5746)
Type: Domain

This is a highly conserved domain found in various Platyhelminthes. Its function is currently unknown, with some of the sequences annotated as being Palmitoyltransferase. This highly conserved domain is located at the amino terminus, next to a DHHC domain (named for its signature tetrapeptide Asp-His-His-Cys).
Vanin, C-terminal (Vanin_C)
Type: Domain

Biotinidase catalyses the hydrolysis of biocytin, the product of biotin-dependent carboxylase degradation, to biotin and lysine. Biotinidase deficiency is an inherited metabolic disorder of biotin recycling that is characterised by neurological and cutaneous abnormalities, and can be successfully treated with biotin supplementation .

Pantetheinase is an enzyme that hydrolyses pantetheine, an intermediate metabolite of coenzyme A, into pantothenic acid (vitamin B5) and cysteamine. The pantetheinase family consists of pantetheinase/vanin-1/VNN1, GPI-80/VNN2 and vanin-3/VNN3. VNN2 and VNN3 are expressed in human leukocytes .

Both mammalian biotinidase and pantetheinase share a carbon-nitrogen hydrolase domain with significant similarity to the photoprotein from oceanic squid symplectin .

This domain is found at the C terminus of Vanin 1 and related proteins, including biotinidase/VNN family members .
Ta1207 family (Ta1207)
Type: Family

The function of this family is unknown. The protein forms a homopentameric complex in T. acidophilum . Each protein is composed of two structurally similar domains .
CRISPR system CMR subunit Cmr7 1 (Cmr7A)
Type: Family

In the CRISPR-Cas system, RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse "payload" of targeting crRNA. This entry represents the Cmr7 subunit of the CMR complex .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Protein of unknown function DUF5748 (DUF5748)
Type: Family

The function of this family of euryarchaeal proteins is unknown.
Protein of unknown function DUF5749 (DUF5749)
Type: Family

The function of this family of euryarchaeal proteins is unknown. The structure of this protein forms a β barrel.
Protein of unknown function DUF5750 (DUF5750)
Type: Family

The function of this family of proteins is unknown.
Domain of unknown function DUF5751 (DUF5751)
Type: Domain

The function of this domain found in archaeal proteins is unknown.
TraG, P-loop domain (P-loop_TraG)
Type: Domain

This entry represents the P-loop domain found in the TraG conjugation protein (also known as Type IV (T4S) secretion system-coupling protein VirD4) and related proteins such as VirB4 . T4S system is composed of VirB1-11 and VirD4 proteins, thus, known as VirB/D T4S system and is responsible of protein delivery into host cells, DNA transfer and toxin release, important for survival and pathogenesis. VirB4, VirB11, and VirD4 are cytoplasmic ATPases that provide energy for substrate transfer. VirD4 is also termed coupling protein as it recruits T4S system substrates to the VirB1-11 secretion channel. VirB4 is the most conserved member of the T4S and essential for the system functions. This domain is also found CAG pathogenicity island protein 23 (CagE) from Helicobacter pylori, another example of Type IV secretion system which translocates effector proteins into gastric epithelial cells .
Nuclear cap-binding complex subunit CBP66, C-terminal domain (CBP66_C)
Type: Domain

This entry represents the C-terminal domain of CBP66 subunit of the trypanosoma nuclear cap-binding complex and appears to contain an unusual zinc finger motif (CCCH). CBP66 is part of the complex that recognises this cap .

In protozoa of the family Trypanosomatidae RNA polymerase II (Pol II) generates polycistronic pre-mRNAs which are then processed by trans-splicing and polyadenylation to produce monocistronic mature mRNAs. Trans-splicing transfers the 39-nucleotide (nt)-long capped spliced leader (SL) from the SL RNA to the 5' end of mRNAs. The mRNA cap in these organisms has the unusual feature of containing, in addition to 7-methylguanosine, four modified nucleotides making it by definition a cap 4 structure (m7equation M2AmpAmpCmpm3Um) which appears to be conserved across this family. This highly modified cap is essential for utilisation of the SL RNA during the trans-splicing process, a key event in RNA metabolism . In yeast and human cells, nuclear cap binding complexes (CBCs) consists of two subunits, cap binding proteins 20 and 80 (CBP20 and CBP80), the first being highly conserved from yeast to humans and contains an RNA binding motif. In Trypanosomatidae family, this complex consists of five subunits, the highly conserved CBP20 subunit, an alpha-importin which imports the complex from the cytoplasm similar to the yeast and human counterparts and three subunits that appear to be unique for this family of organisms, namely CBP30, CBP66 and CBP110 . The CBC complex in trypanosomatids are essential for cell viability.
Nuclear cap-binding complex subunit CBP110 (CBP110)
Type: Family

In protozoa of the family Trypanosomatidae RNA polymerase II (Pol II) generates polycistronic pre-mRNAs which are then processed by trans-splicing and polyadenylation to produce monocistronic mature mRNAs. Trans-splicing transfers the 39-nucleotide (nt)-long capped spliced leader (SL) from the SL RNA to the 5' end of mRNAs. The mRNA cap in these organisms has the unusual feature of containing, in addition to 7-methylguanosine, four modified nucleotides making it by definition a cap 4 structure (m7equation M2AmpAmpCmpm3Um) which appears to be conserved across this family. This highly modified cap is essential for utilisation of the SL RNA during the trans-splicing process, a key event in RNA metabolism . In yeast and human cells, nuclear cap binding complexes (CBCs) consists of two subunits, cap binding proteins 20 and 80 (CBP20 and CBP80), the first being highly conserved from yeast to humans and contains an RNA binding motif. In Trypanosomatidae family, this complex consists of five subunits, the highly conserved CBP20 subunit, an alpha-importin which imports the complex from the cytoplasm similar to the yeast and human counterparts and three subunits that appear to be unique for this family of organisms, namely CBP30, CBP66 and CBP110 . The CBC complex in trypanosomatids are essential for cell viability.

This entry represents the CBP110 subunit of the trypanasome nuclear cap-binding complex. CBP110 is part of the complex that recognises this cap.
Nuclear cap-binding complex subunit CBP30 (CBP30)
Type: Family

In protozoa of the family Trypanosomatidae RNA polymerase II (Pol II) generates polycistronic pre-mRNAs which are then processed by trans-splicing and polyadenylation to produce monocistronic mature mRNAs. Trans-splicing transfers the 39-nucleotide (nt)-long capped spliced leader (SL) from the SL RNA to the 5' end of mRNAs. The mRNA cap in these organisms has the unusual feature of containing, in addition to 7-methylguanosine, four modified nucleotides making it by definition a cap 4 structure (m7equation M2AmpAmpCmpm3Um) which appears to be conserved across this family. This highly modified cap is essential for utilisation of the SL RNA during the trans-splicing process, a key event in RNA metabolism . In yeast and human cells, nuclear cap binding complexes (CBCs) consists of two subunits, cap binding proteins 20 and 80 (CBP20 and CBP80), the first being highly conserved from yeast to humans and contains an RNA binding motif. In Trypanosomatidae family, this complex consists of five subunits, the highly conserved CBP20 subunit, an alpha-importin which imports the complex from the cytoplasm similar to the yeast and human counterparts and three subunits that appear to be unique for this family of organisms, namely CBP30, CBP66 and CBP110 . The CBC complex in trypanosomatids are essential for cell viability.

This entry represents the CBP30 subunit of the trypanasome nuclear cap-binding complex. CBP30 is part of the complex that recognises this cap.
SGNH domain (SGNH)
Type: Domain

This domain is usually fused to the membrane domain of the Acyltransferase family (AT3) members.
MAP3K, PH domain (MAP3K_PH)
Type: Domain

Apoptosis signal-regulating kinases (ASK1/2/3 or MAP3K5/6/15) are mitogen-activated protein kinase kinase kinases (MAP3Ks) that mediate cellular responses to redox stress and inflammatory cytokines and play a key role in innate immunity and viral infection. This kind of signalling kinases are regulated by oligomerization and regulatory domains. In its N-terminal there is a thioredoxin-binding domain that negatively regulates activity and a TNF receptor-associated factors (TRAFs)-binding domain which triggers ASK activation and kinase activity. TRAFs-binding domain is composed by 14 helices, which form seven tetratricopeptide repeats (TPRs), followed by a PH-like domain to complete de central regulatory domain of ASK. The central regulatory region promotes ASK1 activity via its PH domain but also facilitates ASK1 autoinhibition by bringing the thioredoxin-binding and kinase domains into close proximity. The PH-like domain, adjacent to the kinase domain, is required together with an intact TPR region for ASK1 activity.

The major role of the central regulatory region is to bring the thioredoxin-binding domain into close proximity to the kinase domain to inhibit its activity .

This PH-like domain is found in the regulatory region of ASK1/2/3 (also known as MAP3K5/6/15). The central regulatory region of ASK1 mediates a compact arrangement of the kinase and thioredoxin-binding domains which allows the binding of substrates for phosphorylation. This PH-like domain adopts the typical form of two antiparallel β-sheets followed by a C-terminal amphipathic helix .