SII-SWORD/CoKE huggingface dataset:
FUZ/MON1/HPS1, third Longin domain (FUZ/MON1/HPS1_longin_3)
Type: Domain

This entry represents the third Longin domain of FUZ, MON1 and HPS1 proteins.

Longin domains are evolutionarily conserved regions widely distributed among eukaryotes, involved in membrane dynamic regulation and exhibit similarities in primary sequence and secondary structure. Longin-like domains are found in FUZ and related proteins, such as the MON1 and HPS1 proteins . The MON1/CCZ1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking . The HPS1/HPS4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules . Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia . Structurally, these domains are composed of an α/β fold which contains five anti-parallel β-strands organised as a central β-sheet and around it, two α-helices .
FUZ/MON1/HPS1, second Longin domain (FUZ/MON1/HPS1_longin_2)
Type: Domain

Longin domains are evolutionarily conserved regions widely distributed among eukaryotes, involved in membrane dynamic regulation and exhibit similarities in primary sequence and secondary structure. Longin-like domains are found in FUZ and related proteins, such as the MON1 and HPS1 proteins . The MON1/CCZ1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking . The HPS1/HPS4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules . Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia . Structurally, these domains are composed of an α/β fold which contains five anti-parallel β-strands organised as a central β-sheet and around it, two α-helices .

This entry represents the second Longin domain found in FUZ, MON1 and HPS1 proteins.
FUZ/MON1/HPS1, first Longin domain (FUZ/MON1/HPS1_longin_1)
Type: Domain

Longin domains are evolutionarily conserved regions widely distributed among eukaryotes, involved in membrane dynamic regulation and exhibit similarities in primary sequence and secondary structure. Longin-like domains are found in FUZ and related proteins, such as the MON1 and HPS1 proteins . The MON1/CCZ1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking . The HPS1/HPS4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules . Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia . Structurally, these domains are composed of an α/β fold which contains five anti-parallel β-strands organised as a central β-sheet and around it, two α-helices .

This entry represents the first Longin domain found in FUZ, MON1 and HPS1 proteins.
CCN, TSP1 domain (TSP1_CCN)
Type: Domain

Proteins from the CCN family are intercellular signalling proteins that includes six homologous members: cysteine-rich 61(Cyr61)/CCN1, connective tissue growth factor (Ctgf)/CCN2, nephroblastoma overexpressed gene (Nov)/CCN3, Wnt-induced secreted protein 1 (Wisp1)/CCN4, Wisp2/CCN5, and Wisp3/CCN6. They are involved in many biological processes, such as angiogenesis, wound healing, and tumorigenesis, by regulating the proliferation, migration, and differentiation of the target cells . They interact with extracellular matrix components and growth factors via one of their four domains. In particular CNN3 (previously known as Nov) plays an important role in the generation of various types of tissues, such as muscle, fat, cartilage, and bone. CCN3 is expressed in notochord and presomitic mesoderm in early stage development, and in adults it is expressed in diverse tissues, including the nervous system, muscle, cartilage, and bone .

This entry represents a sub-type of thrombospondin module 1 (TSP1) domains found in matricellular CCN proteins which shares a similar three-stranded fold with the thrombospondin type 1 repeats of thrombospondin-1 and spondin-1. This domain has an alternative disulphide binding pattern compared to the canonical TSP1 domain and a conserved charged cluster in the centre of the domain which suggests to have a potential functional binding site for heparan sulfate .
Golgin subfamily A, conserved domain (GOLGA_cons_dom)
Type: Domain

This entry represents the conserved domain found in the Golgin subfamily A members. This domain is comprised of coiled-coil in GM130 (GOLGA2) and related proteins .

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 .
Protein of unknown function DUF5759 (DUF5759)
Type: Family

This is a family of uncharacterised proteins of unknown function found mostly in viruses.
Domain of unknown function DUF5741 (DUF5741)
Type: Domain

This coiled-coil is found in various Platyhelminthes, with many of the sequences annotated as being uveal autoantigen with coiled-coil. This region is one of the numerous coiled-coil regions which constitutes this antigen. The function is currently unknown.
Domain of unknown function DUF5742 (DUF5742)
Type: Domain

This is a highly conserved domain of unknown function found in various Platyhelminthes.
CCZ1/INTU/HSP4, first Longin domain (CCZ1/INTU/HSP4_longin_1)
Type: Domain

Longin domains are evolutionarily conserved regions widely distributed among eukaryotes, involved in membrane dynamic regulation and exhibit similarities in primary sequence and secondary structure. Longin-like domains are found in FUZ and related proteins, such as the MON1 and HPS1 proteins . The MON1/CCZ1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking . The HPS1/HPS4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules . Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia . Structurally, these domains are composed of an α/β fold which contains five anti-parallel β-strands organised as a central β-sheet and around it, two α-helices .

This entry represents the first Longin domain found in INTU, CCZ1 and HPS4.
CCZ1/INTU, second Longin domain (CCZ1/INTU_longin_2)
Type: Domain

Longin domains are evolutionarily conserved regions widely distributed among eukaryotes, involved in membrane dynamic regulation and exhibit similarities in primary sequence and secondary structure. Longin-like domains are found in FUZ and related proteins, such as the MON1 and HPS1 proteins . The MON1/CCZ1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking . The HPS1/HPS4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules . Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia . Structurally, these domains are composed of an α/β fold which contains five anti-parallel β-strands organised as a central β-sheet and around it, two α-helices .

This entry represents the second Longin domain found in INTU and CCZ1 proteins.
CCZ1/INTU/HPS4, third Longin domain (CCZ1/INTU/HSP4_longin_3)
Type: Domain

Longin domains are evolutionarily conserved regions widely distributed among eukaryotes, involved in membrane dynamic regulation and exhibit similarities in primary sequence and secondary structure. Longin-like domains are found in FUZ and related proteins, such as the MON1 and HPS1 proteins . The MON1/CCZ1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking . The HPS1/HPS4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules . Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia . Structurally, these domains are composed of an α/β fold which contains five anti-parallel β-strands organised as a central β-sheet and around it, two α-helices .

This entry represents the third Longin domain found in CCZ1, INTU and HPS4 proteins.
Autochaperone domain type 1 (AC_1)
Type: Domain

This entry represents the autochaperone domain of type 1 (AC-1) in the Type Va Secretion System (T5aSS). Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharide diderm bacteria (archetypical Gram-negative bacteria). The AC of type 1 with β-fold appears as a prevalent and conserved structural element exclusively associated to β-helical AT passenger .
Recombination directionality factor-like (Gp3-like)
Type: Family

This entry includes Gp3 from Streptomyces phage phiC31. Gp3 is a recombination directionality factor that interacts directly with the integrase tetramer to activate excision and inhibit integration . The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Transglycosylase SLT domain 3 (SLT_3)
Type: Domain

This entry represents a lysozyme like domain found predominantly in bacteria. The domain contains several conserved cysteine and histidine residues suggesting that it may bind to zinc. This domain is related to the SLT domain 1.
Type IV secretion system pilin (T4SS_pilin)
Type: Family

Proteins in this entry are predicted to be Type IV secretion system pilins.
Bacterial toxin, RNase RnlA/LsoA, DBD domain (RnlA/LsoA-toxin_DBD)
Type: Domain

Toxin/antitoxin (TA) systems are highly conserved among bacteria and archaea. They play a role in plasmid maintenance, biofilm formation, persister cell formation, general stress response, and phage defense and consist of a stable toxin and an unstable antitoxin. Toxins RnlA (RNase LS) and LsoA are type II TA systems that play a role in phage defence . RnlA and LsoA have endoribonuclease activity, activated after bacteriophage T4 infection. RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralised by the activity of the unstable antitoxin RnlB .

The crystal structure of RnlA revealed that it consist of an N-terminal domain (NTD), an N-Repeated Domain (NRD) and a Dmd-Binding Domain (DBD), being this structure unique and different from all known toxin structures .

This entry represents the C-terminal DBD domain of RnlA and LsoA bacterial toxins, responsible for the RNA cleavage activity and toxicity. Through interaction between DBDs, RnlA dimerises in solution. T4 Dmd binds to DBD for inhibition of RnlA toxicity and RnlB also inhibits the toxicity of DBD .
Putative phage metallopeptidase (Put_Metallopep)
Type: Domain

This entry represents a probable metallopeptidase domain found in a variety of phage and bacterial proteomes.
Phage tail tube protein-like (Phage_tube_2)
Type: Family

This family of proteins are tube proteins which polymerise to form the phage tails. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Spondin-like TSP1 domain (TSP1_spondin_dom)
Type: Domain

This entry represents a sub-type of TSP1 domain that have an alternative disulphide binding pattern compared to the canonical TSP1 domain . This domain is found in Spondin and related proteins.
Double zinc ribbon domain (DZR_2)
Type: Domain

This domain consists of two zinc ribbon motifs and is approximately 60 amino acids in length. This domain can be found at the N terminus of the ComF operon protein 3.
Fructose-1-6-bisphosphatase class 1, C-terminal (FBPase_C_dom)
Type: Domain

Fructose-1,6-bisphosphatase (FBPase) is a critical regulatory enzyme in gluconeogenesis that catalyses the removal of 1-phosphate from fructose 1,6-bis-phosphate to form fructose 6-phosphate . Five different classes (or types) of FBPases have been identified based on their amino acid sequences, with class I most widely distributed among living organisms .

This domain can be found at the C terminus of the FBPase class 1 family members. According to ECOD this domain has a Rossmann-like fold.
Bacterial Ig-like domain 13 (Big_13)
Type: Domain

This entry represents a presumed domain found as tandem repeats of high sequence identity in bacterial cell surface proteins.
Cyanophycin synthase-like, N-terminal (Cyanophycin_syn_N)
Type: Domain

Cyanophycin is an insoluble storage polymer for carbon, nitrogen, and energy, found in most Cyanobacteria. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine. The polymer is made by this enzyme, cyanophycin synthetase, and degraded by cyanophycinase. Heterologously expressed cyanophycin synthetase in Escherichia coli produces a closely related, water-soluble polymer with some Arg replaced by Lys. It is unclear whether enzymes that produce soluble cyanophycin-like polymers in vivo in non-Cyanobacterial species should be designated as cyanophycin synthetase itself or as a related enzyme. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions .

This domain is found at the N terminus of cyanophycin synthase proteins and related enzymes from bacteria and archaea.
Protein of unknown function DUF5676 (DUF5676)
Type: Family

This family of presumed integral membrane proteins is found in bacteria and archaea. Proteins in this family are approximately 90 amino acids in length and contain two predicted transmembrane helices.
Glycosyl-4,4'-diaponeurosporenoate acyltransferase (CrtO)
Type: Family

This family of proteins is found in certain bacterial lineages. In staphylococcus this protein is known to be Glycosyl-4,4'-diaponeurosporenoate acyltransferase, an enzyme involved in the final step of synthesis of staphyloxanthin, an orange pigment found in most S. aureus strains. Members of the family contain and EXXH motif that may be functionally important .
Ig-like domain CHU_C associated (Ig_7)
Type: Domain

This entry represents a presumed Ig-like domain found as tandem repeats in proteins with the gliding motility-associated C-terminal domain CHU_C.
Atypical Rib domain (aRib)
Type: Domain

This entry represents the atypical Rib (aRib) domain found in a variety of bacterial cell surface proteins. These proteins share a conserved motif with the Rib domain (YPDXXD). The structure of the aRib domain has been solved from two proteins, the SrpA adhesin and the GspB adhesin . In these proteins this domain has been termed the unique domain due to its lack of similarity to any other known structures at the time. The aRib domain from SrpA has been shown to mediate a dimer interaction .
TssC1, N-terminal (TssC1_N)
Type: Domain

The long cytoplasmic tubular structure of the T6SS system is wrapped by a sheath structure composed of two proteins, TssB and TssC. Contraction of the sheath causes the internal tube of the T6SS with associated effectors to be propelled out of the effector cell and across the membranes of bacterial or eukaryotic target cells .

TssB and TssC assemble into tubular structures with cogwheel patterns resembling the bacteriophage contractile sheath . Several structures of T6SS sheath assemblies have been solved displaying a helical assembly . Interactions between TssB and TssC occur between the N-terminal region of TssC and the conserved a-helix of TssB . The two proteins of the F. novicida T6SS outer sheath, IglA (TssB) and IglB (TssC), are interdigitated into a single fold similar to that of the phage sheath. The F. novicida T6SS outer sheath has a highly interlaced two-dimensional array architecture with augmented β sheets that is essential to secretory function .

Three distinct T6SS subtypes exist, T6SSi, in which most proteobacterial T6SSs are found, including V. cholerae and P. aeruginosa; T6SSii for the Francisella T6SS; and T6SSiii for Bacteroidetes systems .

TssB/TssC are also known as IglA/IglB and VipA/VipB.

This entry represents the N-terminal domain of TssC1, a type VI secretion system sheath protein.
TssC1, C-terminal (TssC1_C)
Type: Domain

The long cytoplasmic tubular structure of the T6SS system is wrapped by a sheath structure composed of two proteins, TssB and TssC. Contraction of the sheath causes the internal tube of the T6SS with associated effectors to be propelled out of the effector cell and across the membranes of bacterial or eukaryotic target cells .

TssB and TssC assemble into tubular structures with cogwheel patterns resembling the bacteriophage contractile sheath . Several structures of T6SS sheath assemblies have been solved displaying a helical assembly . Interactions between TssB and TssC occur between the N-terminal region of TssC and the conserved a-helix of TssB . The two proteins of the F. novicida T6SS outer sheath, IglA (TssB) and IglB (TssC), are interdigitated into a single fold similar to that of the phage sheath. The F. novicida T6SS outer sheath has a highly interlaced two-dimensional array architecture with augmented β sheets that is essential to secretory function .

Three distinct T6SS subtypes exist, T6SSi, in which most proteobacterial T6SSs are found, including V. cholerae and P. aeruginosa; T6SSii for the Francisella T6SS; and T6SSiii for Bacteroidetes systems .

TssB/TssC are also known as IglA/IglB and VipA/VipB.

This entry represents the C-terminal domain of TssC1, a type VI secretion system sheath protein.
GpV-like, apex motif (GpV-like_apex)
Type: Conserved_site

This entry represents a short motif found at the C terminus of Phage gpV proteins. These proteins act as a spike for piercing the host membrane. The apex motif contains a conserved HXH motif that coordinates an iron ion .
Nascent polypeptide-associated complex subunit alpha-like, UBA domain (NAC-like_UBA)
Type: Domain

This entry represents the UBA domain found at the C-terminal of the Nascent polypeptide-Associated Complex (NAC) subunit alpha. This domain is also found in HYPK (Huntingtin-interacting protein K) in which mediates a constitutively protein interaction with Naa15 auxiliary subunit from N-terminal acetyltransferase NatA. NatA associates with the ribosome and nascent polypeptides, suggesting that HYPK also interacts with these polypeptides possibly to facilitate Nt-acetylation fidelity .

In eukaryotes, the Nascent polypeptide-Associated Complex (NAC) is a heterodimeric cytosolic protein complex composed of alpha and beta subunits. NAC binds reversibly to the ribosome where it is in contact with nascent chains as they emerge from the ribosome and protects them against inappropriate interaction with cytosolic factors. However, the cellular function of NAC seems to be much more diverse as it is also involved in transcription regulation and mitochondrial translocation . Alpha and beta NACs share homology with each other, both contain a NAC A/B domain, responsible for the complex dimerisation. In archaea no beta NAC proteins are found; the complex is an homodimer of NAC alpha . These proteins have an additional ubiquitin-associated (UBA) domain which suggests the involvement of NAC in the cellular protein quality control system via the ubiquitination pathway .
Domain of unknown function DUF5698 (DUF5698)
Type: Domain

DUF5698 can be found at the N terminus of a group of proteins from bacteria and archaea. Their C-terminal transmembrane helix contains a GXXXGXXXG motif which is characteristic of transmembrane helices that dimerise.
Protein of unknown function DUF5752 (DUF5752)
Type: Family

This family describes proteins of unknown function. It includes the uncharacterised protein OrfY from the hyperthermophilic archaeum Thermoproteus tenax, a protein that co-occurs with the treS/P protein in an operon regulating the synthesis of trehalose. The structure of this protein shows it contains an internal duplication .
FANCL, UBC-like domain 3 (FANCL_d3)
Type: Domain

This entry represents the third of three UBC-like domains found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits encoded by the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2 .
dATP/dGTP diphosphohydrolase, N-terminal (dATP/dGTP_diPOhydrolase_N)
Type: Domain

This entry represents the N-terminal region of dATP/dGTP diphosphohydrolase (SHab15497_00040), an Acinetobacter phage protein that catalyses the hydrolysis of dGTP into dGMP, which is needed among others for the first step of biosynthesis of dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate) .
Domain of unknown function DUF5745 (DUF5745)
Type: Domain

This is a domain of unknown function with homology to the CH domain. This domain can be found in CEP95

CEP95 is localised to the centrosome and the spindle pole . Its function is not clear. It is phosphorylated upon DNA damage, probably by ATM or ATR .
Domain of unknown function DUF5744 (DUF5744)
Type: Domain

This is a highly conserved domain found in various Platyhelminthes. The function is currently unknown.
Domain of unknown function DUF5743 (DUF5743)
Type: Domain

This is a highly conserved domain found in various Platyhelminthes. The function is currently unknown.