SII-SWORD/CoKE huggingface dataset:
Eisosome protein 1 (Eisosome1)
Type: Family

This family of fungal proteins represents the eisosome 1 family. Eisosome protein 1 is required for normal formation of eisosomes, large cytoplasmic protein assemblies that localize to specialised domains on plasma membrane and mark the site of endocytosis .
Threonine/Serine exporter, ThrE (ThrE_2)
Type: Domain

This domain is found in a group of membrane proteins involved in the export of threonine and serine. L-threonine, L-serine are both substrates for the exporter. The exporter exhibits nine-ten predicted transmembrane-spanning helices with long charged C and N termini and an amphipathic helix present within the N terminus . L-Threonine can be made by the amino acid-producing bacterium Corynebacterium glutamicum, but the potential for amino acid formation can be considerably improved by reducing its intracellular degradation into glycine and increasing its export by this exporter .

Proteins containing this domain are found in Bacteria, Archaea, and the fungal kingdoms, and the family can exist either as a single long polypeptide chain or as two short polypeptides . All members show an extended hydrophilic N-terminal domain with weak sequence similarity to portions of hydrolases (proteases, peptidases, and glycosidases); this suggests that since this region is cytoplasmic to the membrane it may be generating the transport substrate, so may imply that threonine may not be the primary substrate and the ThrE has a subsidiary function .
ECF transporter, substrate-specific component (ECF_trnsprt_substrate-spec)
Type: Family

Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component), and an energy-coupling module . The substrate-binding component is a small integral membrane protein which captures specific substrates and forms an active transporter in the presence of the energy-coupling AT module. The energy coupling module is composed of an ATPase typical of the ATP binding cassette (ABC) superfamily (A component) and a characteristic transmembrane protein (T component). Unlike the ABC transporters, an energy coupling module can be shared between multiple different substrate-binding components.

This entry represents the substrate-specific component from a number of different ECF transporters.
Putative quorum-sensing-regulated virulence factor (QSregVF_b)
Type: Family

This is a family of short Pseudomonas proteins that are potential virulence factors. The structure of

, a secreted protein that belongs to

, has been solved and deposited as

. It is predicted that these two adjacent proteins form a single transcriptional unit based on the prediction that together they interact with their adjacent protein PotD, which is the putrescine-binding periplasmic protein in the polyamine uptake system comprising PotABCD. These two adjacent proteins are predicted to be quroum-sensing-regulated virulence factors .
Erythronate-4-phosphate dehydrogenase, dimerisation domain (Erythronate-4-P_DHase_dimer)
Type: Domain

This entry represents the dimerisation domain found at the C-terminal of erythronate-4-phosphate dehydrogenases .
Protein of unknown function DUF3830 (DUF3830)
Type: Family

This is a family of bacterial and archaeal proteins. The structure of one of family members,

, has been characterised and shown to contain a cyclophilin-like fold.
Protein of unknown function DUF3834 (DUF3834)
Type: Family

This family is likely to be related to solute-binding lipo-proteins.
Wadjet protein JetD, C-terminal (JetD_C)
Type: Domain

This is a domain found at the C-terminal of Wadjet protein JetD from Bacillus cereus. JetD is a component of the antiplasmid transformation system Wadjet type I, composed of JetA, JetB, JetC and JetD. Expression of Wadjet type I in B.subtilis (strain BEST7003) reduces the transformation efficiency of plasmid pHCMC05 . This domain is structurally similar to DNA topoisomerases, therefore, it may be a DNA-binding domain.
Rhamnogalacturonase A/B/Epimerase-like, pectate lyase domain (RHGA/B-epi-like_pectate_lyase)
Type: Domain

This domain posses a β-helical structure like pectate lyase, found in a varied group of proteins including D-mannuronate C5-epimerases and glycosyl hydrolases from GH family 28. This domain is also found in Non-secreted LysM effector LysM15 and LysM19 from Penicillium expansum, which might be involved in manipulation of host defenses for successful infection .
Domain of unknown function DUF3322 (DUF3322)
Type: Domain

This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N terminus.
Protein of unknown function DUF3878 (DUF3878)
Type: Family

This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture .
Protein of unknown function DUF3877 (DUF3877)
Type: Family

This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture .
Protein of unknown function DUF3879 (DUF3879)
Type: Family

This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture .
Protein of unknown function DUF3881 (DUF3881)
Type: Family

This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture .
Domain of unknown function DUF3880 (DUF3880)
Type: Domain

This entry represents a domain whose function is not known. The Eubacterium rectale gene encoding this domain appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture . This domain is also found at the N-terminal of spore protein YkvP from B. subtilis.

CgeB is a putative glycosyltransferase involved in the glycosylation of the Bacillus subtilis endospore crust . It is co-expressed with CgeA and CgeD, which are also implicated in crust glycosylation. The crust polysaccharide layer, which CgeB likely contributes to, consists of rhamnose- and galactose-related variants and may contain rare sugars. This glycosylation could protect the crust against biological degradation and scavenging .

YkvP is a spore protein that contains a motif conserved among cell wall binding proteins. Its expression is dependent on both SigK and GerE transcription factors. YkvP is intrinsic to mature spores. The conserved motif in YkvP is thought to function as a kind of signal sequence involved in protein assembly to forespores during sporulation .
Autophagy protein Atg19/Atg34, C-terminal (Atg19/Atg34_C)
Type: Domain

Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are sequestered into double-membrane vesicles to form the autophagosome. The contents of the autophagosome are delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. In contrast to autophagy, the cytoplasm to vacuole transport (Cvt) pathway is a highly selective process that involves the sequestration of at least two specific cargos that are resident vacuolar hydrolases: aminopeptidase I (Ape1) and alpha-mannosidase (Ams1). These proteins are sequestered within a double-membrane vesicle, termed a Cvt vesicle. The Cvt vesicle is fairly consistent in size, and is much smaller than the autophagosome, being 140-160 nm in diameter.

The genes involved in autophagy in yeast are termed autophagy-related (Atg) genes. Autophagy and the Cvt pathway are topologically and mechanistically similar and share most of the Atg components . The precursor of Ape1 (prApe1) is sequestered within either Cvt vesicles or autophagosomes, depending on the nutrient conditions, and delivered to the vacuole.

Atg19 is a peripheral membrane protein with differing binding sites for both Ape1 and Ams1. Atg19 plays a central role in cargo sorting and transport to the vacuole by linking Ams1 and prApe1 to Atg8 and Atg11 .

This entry represents the C-terminal region of Atg19 and homologue Atg34 (Yol083wp) . The Atg8-binding region is thought to be in the very C-terminal residues .
Domain of unknown function DUF3858 (DUF3858)
Type: Domain

This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.
Mto1-like, Mto2p-binding domain (Mto1-like_Mto2p-bd)
Type: Domain

This domain is found at the C terminus of Gamma tubulin complex adapter mto1 and SPC72 from yeast, Anucleate primary sterigmata protein B from Emericella nidulans (ApsB) and similar fungal sequences. Mto1 is an spindle pole body (SPB) component that acts as the gamma-tubulin complex-binding protein of the SPB outer plaque . This entry represents the binding domain for attachment to Mto2p. The interaction of Mto2p with this region of Mto1 is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis .

ApsB is involved in regulation of nuclear migration. It may be involved in regulating nuclear positioning .
Copper type II ascorbate-dependent monooxygenase, C-terminal (Cu2_monoox_C)
Type: Domain

Copper type II, ascorbate-dependent monooxygenases are a class of enzymes that requires copper as a cofactor and which uses ascorbate as an electron donor. This family contains two related enzymes, dopamine-beta-monooxygenase (

) and peptidyl-glycine alpha-amidating monooxygenase (

). There are a few regions of sequence similarities between these two enzymes, two of these regions contain clusters of conserved histidine residues which are most probably involved in binding copper.

This entry represents the C-terminal domain of the enzyme which, like the N terminus has a PNGase F-like fold.
NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi (NADH-UbQ_OxRdtase_su21_C_fun)
Type: Domain

This domain is found in the C-terminal region of fungal NADH-ubiquinone oxidoreductase 21kDa subunits .
TFIIEalpha/SarR/Rpc3 HTH domain (TFIIEa/SarR/Rpc3_HTH_dom)
Type: Domain

The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF .
Aspartate aminotransferase Ic (AspAT_Ic)
Type: Family

Aminotransferases (ATs) are pyridoxal phosphate (PLP)-dependent enzymes that catalyze the reversible transfer of nitrogen from an amino donor to a keto acid amino acceptor. ATs have been classified into five classes by evolutionary relationship. Aspartate aminotransferase (AspAT) belongs to class I ATs. AspAT catalyzes the reaction from L-glutamate and oxaloacetate to L-aspartate and alpha-ketoglutarate .
Domain of Unknown Function DUF3856 (DUF3856)
Type: Domain

This domain of unknown function is found in a small group of tetratricopeptide-like proteins, which includes the uncharacterised protein

. The structure of Q8KAL8 is known and belongs to the SCOP all alpha class, TPR-like superfamily, CT2138-like family.
PX domain-containing protein LEC1-like, C-terminal (LEC1-like_C)
Type: Domain

The function of this domain is not known, and it is found in fungal proteins, including LEC1/YPR097W from budding yeast and C663.15c/C1450.12 from fission yeast. They contain this domain, known as DUF3818 and PXA domains. LEC1 is a phosphoinositide-binding protein that plays a role in regulation of ergosterol distribution in the cell . It facilitates ergosterol transport between plasma membrane and lipid droplets .
PX-associated domain (PX-associated)
Type: Domain

The function of this domain is not known, but it is almost always found N-terminal to a PX domain (

).
Protein of unknown function DUF3599 (DUF3599)
Type: Family

This family of bacterial proteins includes phage-like element PBSX protein xkdH from Bacillus subtilis. The function of the family is unknown.
CCR4-NOT transcription complex subunit 1, domain 4 (CNOT1_dom_4)
Type: Domain

The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1 to Not5), Caf1, Caf40, Caf130 and Ccr4 . The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress . Caf1 and Ccr4, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1, a putative RNA helicase thought to be a component of the decapping complex . Pop2, a component of the Ccr4-Not complex, functions as a deadenylase .

This entry represents a domain of unknown function found in the Not1 subunit of the CCR4-Not complex.
ComZ (ComZ)
Type: Family

ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon .
Domain of unknown function DUF3846 (DUF3846)
Type: Domain

A family of uncharacterised proteins found by clustering human gut metagenomic sequences . In a few cases it is found fused to the C terminus of ArdA (

). ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification .
UPF0313, C-terminal (UPF0313_C)
Type: Domain

This domain tends to occur to the C terminus of a radical SAM domain (

) in members of the uncharacterised protein family UPF0313.
Alpha-1,6-glucosidases, pullulanase-type, C-terminal (Pullul_strch_C)
Type: Domain

This entry represents the uncharacterised C-terminal domain of secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyse alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate.
Uncharacterised protein family YqhG (YqhG)
Type: Family

This family of putative proteins appears to be restricted to Firmicutes. Their function is not known.
Uncharacterised protein family YqhR (YqhR)
Type: Family

This family of proteins is conserved in the Bacillaceae family of the Firmicutes. Their function is not known.
Nitrogenase molybdenum-iron protein beta chain, N-terminal (Nase_Mo-Fe_CF_bsu_N)
Type: Domain

The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene which has an Fe4S4 cluster bound between the subunits and two ATP-binding domains. The Fe protein supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia . Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of the nifNE operon and of some other nif genes . It has been proposed that nifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .

This entry represents the uncharacterised N-terminal domain of the molybdenum-iron protein beta chain, which is part of the nitrogenase complex that catalyses the key enzymatic reactions in nitrogen fixation.
Orexigenic neuropeptide QRFP/P518 (P518)
Type: Family

QRFP/P518 has a direct role in maintaining bone mineral density . QRFP has also found to be important in energy homeostasis by regulating appetite and energy expenditure in mice . The C-terminal 28 residues are the functional neuropeptide 26RFa .
Colicin, receptor domain (Colicin_R_dom)
Type: Domain

Bacteriocins are protein antibiotics that kill bacteria closely related to the producing species. Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism.

Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane .

Colicins are composed of domains with distinct functional roles. In general they contain a central R (receptor) domain that mediates receptor binding, an N-terminal T (translocation) domain that mediates translocation of the protein from the outer membrane receptor to the colicin's target within the cell, and a C-terminal C (catalytic) domain that performs the catalytic cleavage .

This entry represents the central R domain found in colicin-E2 and other colicins.
Ribonuclease HII/HIII domain (RNase_HII/HIII_dom)
Type: Domain

The entry represents the Rnase H type-II domain.

Ribonuclease H (RNase H) (

) is a member of the ribonuclease family, which recognises and cleaves the RNA strand of RNA-DNA heteroduplexes. The enzyme is widely present in all three kingdoms of living organisms, including bacteria, archaea, and eukaryotes, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements . RNases H are classified into two evolutionarily unrelated families, type-I and type-II RNase H, with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. There appears to be three evolutionarily distinct lineages of cellular Rnase H enzymes . Type-I or RNase HI domains have been found in all Eukarya, one Archaea, many Eubacteria, a few non-LTR retroposons and all LTR retrotransposons. Type II enzymes consist of RNase HII (rnhB) and HIII (rnhC), which are homologous enzymes. RNase HII can be found in Archaea, Eubacteria and all Eukarya, while RNase HIII appears only in some Eubacteria. In eukaryotes and all Archaea, RNase HII enzymes may constitute the bulk of all Rnase H activity, while the reverse is true in Eubacteria like E. coli where RNase HI is the major source of RNH activity . All LTR retrotransposons acquired an enzymatically weak RNase H domain that is missing an important catalytic residue found in all other RNase H enzymes. Vertebrate retroviruses appear to have reacquired their RNase H domains, which are catalytically more active, but their ancestral RNase H domains (found in other LTR retrotransposons) have degenerated to give rise to the tether domain unique to vertebrate retrovirus . Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Retroviral RNase H is synthesised as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins.
Ribonuclease HIII, N-terminal (RNase_HIII_N)
Type: Domain

Ribonuclease HIII

cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII .

This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.
Lactate utilization protein B, C-terminal (LutB_C)
Type: Domain

This entry represents the C-terminal domain of Lactate utilization protein B, a family of 4Fe-4S, iron-sulphur cluster binding proteins. These proteins have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulphur clusters.
Murein transglycosylase-C, N-terminal (Murein_transglycosylaseC_N)
Type: Domain

Membrane-bound lytic murein transglycosylase C (also known as murein hydrolase C), is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. This entry represents the N-terminal domain, whose function is currently not known.
ERAP1-like C-terminal domain (ERAP1-like_C_dom)
Type: Domain

This large domain is composed of 16 α helices organised as 8 HEAT-like repeats. This domain forms a concave face that faces towards the active site of the peptidase.
Nickel/cobalt homeostasis protein RcnB (RcnB)
Type: Family

RcnB is a family of Proteobacteria proteins. RcnB is required for maintaining metal ion homeostasis, in conjunction with the efflux pump RcnA, family NicO .
Domain of unknown function DUF3333 (DUF3333)
Type: Domain

This N-terminal domain is functionally uncharacterised and it is found in proteins annotated as putative phosphate ABC transporter permease proteins. This presumed domain is typically between 116 to 159 amino acids in length.
ELMO, armadillo-like helical domain (ELMO_ARM)
Type: Domain

This domain is found in eukaryotes and predominantly in ELMO (Engulfment and cell motility) proteins where it may play an important role in defining the functions of the ELMO family members and may be functionally linked to the ELMO domain in these proteins .
Cloacin/colicin (Cloacin_colicin)
Type: Family

Bacteriocins are protein antibiotics that kill bacteria closely related to the producing species. Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism.

Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane .

Colicins are composed of domains with distinct functional roles. In general they contain a central R (receptor) domain that mediates receptor binding, an N-terminal T (translocation) domain that mediates translocation of the protein from the outer membrane receptor to the colicin's target within the cell, and a C-terminal C (catalytic) domain that performs the catalytic cleavage .

This entry represents the cloacin family of colicins.
Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 (rRNA_MeTfrase_Spb1_DUF3381)
Type: Domain

This uncharacterised domain is found in the central region of fungal SPB1 and mammalian homologue FTSJ3.

SPB1 is an adoMet-dependent rRNA methyltransferase required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit . In Saccharomyces cerevisiae, it specifically methylates the guanosine in position 2922 of the 25S rRNA at the stage of 27S pre-rRNA maturation . It interacts with the snoRNA-associated proteins Nop1 and Nop58 .