SII-SWORD/CoKE huggingface dataset:
Glycoside hydrolase 35, catalytic domain (Gly_Hdrlase_35_cat)
Type: Domain

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 35 (

) comprises enzymes with only one known activity: beta-galactosidase (

). Mammalian beta-galactosidase is a lysosomal enzyme (gene GLB1 ) that cleaves the terminal galactose from gangliosides, glycoproteins, and glycosaminoglycans and whose deficiency is the cause of the genetic disease Gm(1) gangliosidosis (Morquio disease type B). Beta-1,2-glucosyltransferase from gnavibacterium album [

] is classified as part of the GH35 family (

). This enzyme transfers a glucosyl residue from the non-reducing end of a 1,2-beta-D-glucan to a glucose residue of an acceptor molecule, forming a beta(1,2) linkage .
Neutral/alkaline non-lysosomal ceramidase, C-terminal (NEUT/ALK_ceramidase_C)
Type: Domain

Ceramidases play a key role in sphingolipid metabolism by converting the apoptosis-associated lipid ceramide to Sph, a precursor for the proliferative factor S1P. Three families of CDases (acid, neutral, and alkaline) have been identified that are distinguished by their pH optima, subcellular localisation, primary structure, mechanism, and function .

This entry represents the C-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes . The EC classification is

. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This C-terminal tail of the enzyme is highly conserved across all species and may play a role in the interaction of the enzyme with the plasma membranes. The tail is also vital for the stabilisation of the enzyme as a whole .
Coproheme decarboxylase (CHDC)
Type: Family

Coproheme decarboxylases (ChdC) catalyse the hydrogen peroxide-mediated conversion of coproheme to heme b . Its structure has been revealed .
Daxx, N-terminal Rassf1C-interacting domain (Daxx_N)
Type: Domain

The Daxx protein (also known as death domain-associated protein 6) is thought to play a role in apoptosis. Daxx forms a complex with Axin . Daxx is a scaffold protein shown to play diverse roles in transcription and cell cycle regulation. This N-terminal domain folds into a left-handed four-helix bundle (H1, H2, H4, H5) that binds to the N-terminal residues of the tumour-suppressor Rassf1C .
Piezo non-specific cation channel, cap domain (Piezo_cap_dom)
Type: Domain

This is an extracellular domain at the C terminus of Piezo, or FAM38 mechanosensitive non-specific cation channel protein. These proteins form a channel whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents . These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways . Each protomer consists of 38 TM helices that form unusual non-planar blades, and an extracellular cap-like structure, the latter represented in this entry . This domain is embedded in the centre of the trimer and may control the transmembrane constriction site suggested to act as a transmembrane gate . This domain adopts a distinctive β-sandwich fold . Members of this entry are found in animals and plants.
Glycosyl hydrolase family 63, C-terminal (Glyco_hydro_63_C)
Type: Domain

Enzymes belonging to glycosyl hydrolase family 63 (

) catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase

is the first enzyme in the N-linked oligosaccharide processing pathway.

This entry represents the C-terminal catalytic domain .
Cell division control protein 73, C-terminal (CDC73_C)
Type: Domain

CDC73 is an RNA polymerase II accessory factor , and forms part of the Paf1 complex that has roles in post-initiation events . More specifically, crystal structure analysis shows the C terminus to be a Ras-like domain that adopts a fold that is highly similar to GTPases of the Ras superfamily. The C-terminal domain contains a large but comparatively flat surface of highly conserved residues, devoid of ligand. Deletion of the Cdc73 C-domain significantly reduces Paf1C occupancy on active genes, which means that the Cdc73 C-domain plays a role in promoting association of Paf1C with chromatin .

The canonical nucleotide binding pocket is altered in CDC73, and there is no nucleotide ligand, but it contributes to histone methylation and Paf1 complex (Paf1C) recruitment to active genes. Thus, together with Rtf1, it combines to couple Paf1C to elongating polymerase .
KDPG/KHG aldolase, active site 1 (KDPG/KHG_AS_1)
Type: Active_site

4-Hydroxy-2-oxoglutarate aldolase (

) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (

) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the ε-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.

This site contains the active site arginine.
KDPG/KHG aldolase, active site 2 (KDPG/KHG_AS_2)
Type: Active_site

4-Hydroxy-2-oxoglutarate aldolase (

) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (

) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the ε-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.

This site contains the lysine involved in the Schiff-base formation.
Domain of unknown function DUF4942 (DUF4942)
Type: Domain

This is a domain of unknown function found in bacteria.
Ribosomal RNA small subunit methyltransferase F, first C-terminal domain (RsmF_methylt_CI)
Type: Domain

This is the first of two distinct C-terminal domains of the 16S rRNA methyltransferase RsmF. It is necessary for stabilising the catalytic core .
Ribosomal RNA small subunit methyltransferase F, N-terminal (Methyltr_RsmF_N)
Type: Domain

This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N terminus is critical for stabilising the catalytic core of the enzyme .
Meiotically up-regulated gene 163 protein-like (Mug163-like)
Type: Family

This is a family of fungal mitochondrial proteins, including YGR053C from S. cerevisiae, which is still uncharacterised, and meiotically up-regulated gene 163 protein from S. pombe which plays a role in meiosis .
Domain of unknown function DUF5105 (DUF5105)
Type: Domain

This entry represents a domain found in a group of uncharacterised bacterial proteins. Its function is not known. Proteins containing this domain include a putative lipoprotein, ycdA, whose structure has been revealed (PDB:4r4g).
Protein of unknown function DUF5104 (DUF5104)
Type: Family

This is a family of gut microbes of unknown function.
Type 9 secretion system plug protein, N-terminal domain (T9SS_Plug_N)
Type: Domain

This entry includes Bacteroidetes proteins that appear to form a plug in the type 9 secretion system pore . This is the N-terminal (first domain).
DUF2154, N-terminal (DUF2154_N)
Type: Domain

This short domain lies at the N terminus of a group of uncharacterised proteins containing the formerly DUF2154, annotated as cell wall-active antibiotic response proteins. These domains have been named Toast_rack from its structural resemblance. The function of this domain is not clear.
Protein AmpE (AmpE)
Type: Family

AmpE is a family of bacterial regulatory proteins. AmpE in conjunction with AmpD sense the effect of beta-lactam on peptidoglycan synthesis and relay this signal to AmpR. AmpR regulates the production of beta-lactamase .
Azaphilone pigments biosynthesis cluster protein L, N-terminal (PigL_N)
Type: Domain

This entry represents the N-terminal domain of fungal sequences which were previously described as Helo_like, predicted fungal STAND NTPases . This entry includes Azaphilone pigments biosynthesis cluster protein L (PigL) which is part of the gene cluster that mediates the biosynthesis of azaphilone pigments (MonAzPs), a complex mixture of compounds with a common azaphilone skeleton very widely used as food colorants .
General transcription factor TFIIH, subunit Tfb6 (Tfb6)
Type: Family

This entry includes budding yeast Tfb6 protein, which is a subunit of TFIIH complex that facilities dissociation of the Ssl2 helices from TFIIH . This entry also includes fission yeast uncharacterised protein, SPCC1494.09c.
Fungal STAND N-terminal Goodbye domain (Goodbye_dom)
Type: Domain

The Goodbye domain is an N-terminal domain on certain fungal STAND proteins. The exact function is not known .
NWD2, HET-s N-terminal domain (NWD2_N)
Type: Domain

STAND proteins are signal transducing ATPases which undergo ligand-induced oligomerisation. Stand proteins typically feature an N-terminal effector domain, a central nucleotide-binding domain (NACHT) and a C-terminal ligand-binding region that is composed of several leucine-rich repeats (LRRs) . Homology modelling predicts that the N-terminal region of NWD2, a STAND protein, adopts a HET-s-like fold. This entry represents the N-terminal domain on various fungal STAND proteins. Its function is not known .
NACHT-NTPase and P-loop NTPases, N-terminal domain (SesA)
Type: Domain

This entry represents a domain found in the N terminus of P-loop NTPases, NACHT-NTPases and Ankyrin or WD repeat proteins. The exact function is not known .
NACHT-NTPase, sigma domain (NACHT_sigma)
Type: Domain

This entry reprsents a short conserved region found on NACHT-NTPases . The function of this domain is not known.
Bromodomain protein 4, C-terminal (BRD4_CDT)
Type: Domain

This entry represents the short highly conserved C-terminal domain of certain bromodomain proteins, notably Brd4. The Brd4 CTD interacts with the cyclin T1 and Cdk9 subunits of positive transcription elongation factor b (pTEFb) complex. Brd4 displaces negative regulators, the HEXIM1 and 7SKsnRNA complex, from pTEFb, thereby transforming it into an active form that can phosphorylate RNA pol II .
YBL010C/LAA2-like (YBL010C/LAA2-like)
Type: Family

This is a family of fungal sequences, including YBL010C (also known as LAA2) from S. cerevisiae and its orthologue from S. pombe, C8E11.05c. LAA2 is a clathrin adaptor (adaptin) accessory protein that physically interacts with and is involved in localization of clathrin adaptor protein complex-1 (AP-1) .
Stealth protein CR4, conserved region 4 (Stealth_CR4)
Type: Domain

This entry represents a fourth conserved region on stealth proteins from animals and bacteria. There are four CR regions on mammalian members. CR4 carries a well-conserved CLND sequence-motif. The domain is found in tandem with CR1, CR2 and CR3 on both potential metazoan hosts and on pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains also appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system .
Stealth protein CR3, conserved region 3 (Stealth_CR3)
Type: Domain

This entry represents the third of several highly conserved regions on stealth proteins from animals and bacteria. There are up to four CR regions on all member proteins. The domain is found in tandem with CR1, CR2 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system .
Stealth protein CR1, conserved region 1 (Stealth_CR1)
Type: Domain

This entry represents the first of several highly conserved regions on stealth proteins in metazoa and bacteria. There are up to four CR regions on all member proteins. CR1 carries a well-conserved IDVVYT sequence-motif. The domain is found in tandem with CR2, CR3 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system .
NWD NACHT-NTPase, N-terminal (NACHT_N)
Type: Domain

This is an N-terminal domain on putative NWD NACHT proteins, signal transducing ATPases which undergo ligand-induced oligomerisation .
Tryptophan transporter TrpP (TrpP)
Type: Family

TrpP is a bacterial transmembrane protein that is probably involved in tryptophan uptake. Its expression is regulated by tryptophan-activated RNA-binding regulatory protein (TRAP) .
Outer kinetochore KNL1 complex subunit Kre28 (Kre28)
Type: Family

S.cerevisiae Kre28 is a subunit of a kinetochore-microtubule binding complex that bridges centromeric heterochromatin and kinetochore MAPs and motors . It may be regulated by sumoylation .

Kre28 forms a heterotrimeric complex with Spc105 and this complex is the third linker complex that, along with the Ndc80 and MIND linker complexes, is responsible for bridging between centromeric heterochromatin and kinetochore MAPs and motors . Kre28-Spc105 interaction is important for Spc105 protein turn-over and essential for their mutual recruitment at the kinetochores .
Protein BNIP5 (BNIP5)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 618 and 652 amino acids in length.
Transmembrane protein 252 (TMEM252)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 182 amino acids in length. Their function is not known.
Germinal centre-associated lymphoma protein (GC_assoc_lym)
Type: Family

HGAL (human germinal centre-associated lymphoma, also known as a germinal centre-expressed transcript 2 or germinal centre-associated signalling and motility protein) is part of a family of mammalian sequences typically between 104 and 179 amino acids in length. Members were discovered in a search for proteins precipitating diffuse large B-cell lymphomas . HGAL and its murine homologue, M17 protein, are specifically expressed in germinal centre (GC) B-lymphocytes .

HGAL interacts with the cytoskeleton and aids the activity of interleukin-6 on cell migration . It also modulates the RhoA signalling pathway . HGAL protein also regulates B-cell receptor (BCR) signalling . It seems that membrane-bound and cytoplasmic HGAL regulates distinct biological processes in B-cells.
Ciliary microtubule inner protein 6 (CMIP6)
Type: Family

This family of proteins includes human protein C2orf73 (also known as Ciliary microtubule inner protein 6, CMIP6) and homologues. CMIP6 is a close homologue of C. reinhardtii FAP363. FAP363 contains Mn repeats that make close contacts with the luminal microtubule lattice. Proteins in this family are found in eukaryotes. They are typically between 135 and 289 amino acids in length, with three conserved sequence motifs: GDWWSH, RSDF and KRHG.
Protein of unknown function DUF4663 (DUF4663)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 289 and 334 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important.
Coiled-coil domain-containing protein 24 (CCDC24)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 187 and 319 amino acids in length. There are two completely conserved residues (G and P) that may be functionally important.
Spermatid maturation protein 1, N-terminal (SPEM1_N)
Type: Domain

This entry represents the N-terminal of Spem1. This domain can also be found in human uncharacterised protein C17orf74. Spem1 is exclusively expressed in the cytoplasm of spermatids during the last three steps of spermiogenesis in the mouse testis, and male mice deficient in Spem1 are completely infertile because of deformed sperm .
Proline-rich protein 18 (PRR18)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 297 amino acids in length. The function is not known but there are many highly conserved proline residues.
Altered inheritance of mitochondria protein 3 (Aim3)
Type: Family

Altered inheritance of mitochondria protein 3 (Aim3) was first identified as an actin patch protein . Later, it was found to inhibit barbed-end actin filament elongation . It may be involved in mitochondrion organisation and biogenesis .
Cell-membrane associated Mucin-15 (Mucin-15)
Type: Family

Mucins are heavily glycosylated proteins expressed by various epithelial cell types. They can be divided into two classes according to cellular localisation: membrane-bound mucins and secretory mucins. This entry represents Mucin-15 (MUC15) which is a cell membrane-associated mucin. The predicted protein product of human MUC15 contains an extracelluar domain, a small transmembrane domain, and a highly conserved cytoplasmic tail . Mucin-15 is expressed in human placenta and may play a role in the regulation of trophoblast invasion .
CAMSAP, spectrin and Ca2+/calmodulin-binding region (CAMSAP_CC1)
Type: Conserved_site

This entry represents a conserved region found in calmodulin-regulated spectrin-associated proteins (CAMSAPs) from animals. This conserved region (also known as CC1 region) binds to both spectrin and Ca2+/calmodulin in vitro, although the binding of Ca2+/calmodulin inhibits the binding of spectrin. CC1 appears to be a functional region of CAMSAP1 that links spectrin-binding to neurite outgrowth .

The calmodulin-regulated spectrin-associated (CAMSAP) proteins are defined by a CKK domain that binds microtubules . It includes CAMSAPs from vertebrates and Patronin from invertebrates . CAMSAP1 is the representative member. It contains a conserved region, CC1, that binds to both spectrin and Ca2+/calmodulin in vitro and links spectrin-binding to neurite outgrowth . Patronin binds to and protects the MT minus-end against depolymerization . CAMSAP2 is a key microtubule-organising protein that specifically binds the minus end of non-centrosomal microtubules and regulates their dynamics and organisation. CAMSAP proteins carry an N-terminal region that includes two CH domains represented by

and

, a central region including a predicted coiled-coil, and a C-terminal CKK domain

, which is involved in binding CAMSAP proteins to microtubules .
Circadian-associated transcriptional repressor (Ciart)
Type: Family

Circadian-associated transcriptional repressor (Ciart or Chrono) is a negative regulatory component of the circadian clock . It functions as a transcriptional repressor, modulating BMAL1-CLOCK activity. It also regulates metabolic pathways such as the glucocorticoid response triggered by behavioral stress .
Uncharacterised protein family UPF0715 (UPF0715)
Type: Family

This is a family of Bacilli transmembrane proteins. The function is unknown.
Penicillin-binding protein, N-terminal (PBP_N)
Type: Domain

This domain occurs at the N terminus of some penicillin-binding proteins in Caulobacter species.
Penicillin-binding protein, OB-like domain (PCB_OB)
Type: Domain

This entry represents the OB (oligonucleotide/oligosaccharide binding)-fold domain found in penicillin-binding proteins (PBPs). A. baumannii PBP is the first example of a multimodular PBP containing the OB-fold domain. Structure-based sequence alignment suggests that this OB-fold domain may also exist in high molecular mass PBPs of subclass A1 from other Gram-negative bacteria including the respective PBP1a proteins of P. aeruginosa and K. pneumoniae .
Inovirus G7P protein (Tail_VII)
Type: Family

Tail virion protein 7P is a viral transmembrane protein that interacts with the packaging signal of the viral genome leading to the initiation the virion concomitant assembly-budding process in the host inner membrane.
Small vasohibin-binding protein (SVBP)
Type: Family

Small vasohibin-binding protein (SVBP) acts as a secretory chaperone for VASH1 and contributes to its anti-angiogenic activity . SVBP also interacts with VASH2 and affects its angiogenesis activity .
CLLAC-motif containing domain (CLLAC)
Type: Domain

This short domain is found in chordates. It carries a highly conserved CLLAC sequence motif. The function is not known.
Six6 opposite strand transcript 1 (SIX6OS1)
Type: Family

Protein SIX6OS1 (Six6 opposite strand transcript 1) may be involved in eye development through regulation of the SIX6 transcription factor . It is a meiotic protein that localizes to the central element of the synaptonemal complex and is required for chromosome synapsis during meiotic recombination .
YtcA family (YtcA)
Type: Family

This is a family of bacterial transmembrane proteins. The function is unknown.
Uncharacterised protein YjbT (YjbT)
Type: Family

This is a family of bacterial proteins. The function is unknown.
Uncharacterised protein ycf90 (Ycf90)
Type: Family

Ycf90 is an algal protein located in chloroplasts. Its function is unknown.
Herpesvirus US34A protein family (HHV-5_US34A)
Type: Family

Proteins in this human cytomegalovirus (HHV-5) family contain a transmembrane domain .
Small capsid protein, Herpesviridae (HV_small_capsid)
Type: Family

This is a family of herpes-type viral small capsid proteins, including UL48A (small capsomere-interacting protein or SCP) from human cytomegalovirus . By analogy with SCP from human herpesvirus 1, SCP forms a complex with the major capsid protein in the cytoplasm which is translocated to the nucleus. SCP decorates the outer surface of the capsid shell during capsid assembly, forming a layer between the capsid and the tegument.
Unique cartilage matrix-associated protein (UCMA)
Type: Family

UCMA is a secreted cartilage-specific protein expressed predominantly in resting chondrocytes. It is secreted into the extracellular matrix as an uncleaved precursor and shows the same restricted distribution pattern in cartilage as UCMA mRNA. This protein is proteolytically processed and contains tyrosine sulfates. It seems to be involved in the negative control of osteogenic differentiation of osteochondrogenic precursor cells in peripheral zones of foetal cartilage .
Spindle and centriole-associated protein 1 (SPICE1)
Type: Family

SPICE1 localises to spindle microtubules in mitosis and to centrioles throughout the cell cycle. Deletion of SPICE1 compromises the architecture of spindles, the integrity of the spindle pole and the process of aligning chromosomes on the spindle (chromosome congression) . SPICE1 interacts with CEP120 in centriole duplication and elongation .