SII-SWORD/CoKE huggingface dataset:
Disks large homolog 1-4, PDZ-associated domain (DLG1-4_PDZ_assoc)
Type: Domain

This domain is found between the second and third PDZ domains (

) of Disks large homolog 1-4 (DLG1-4) and similar sequences from vertebrates. Members of this group are involved in synaptic plasticity associated with NMDA receptor signalling .
26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 (Rpn7/CSN1)
Type: Family

This entry includes 26S proteasome regulatory subunit Rpn7 and COP9 signalosome complex subunit 1 (Csn1) and fungal CSN11.

The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae to be required for structural integrity .

The COP9 signalosome is a conserved protein complex composed of eight subunits, where individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control . The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome . COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Polyketide cyclase/dehydrase (Polyketide_cyclase/dehydratase)
Type: Family

This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily .
Metabotropic glutamate receptor, Homer-binding domain (Metabotropic_Glu_rcpt_Homer-bd)
Type: Domain

This entry represents the proline-rich region of metabotropic glutamate receptor proteins that bind Homer-related synaptic proteins.

Metabotropic glutamate receptors function as receptors for glutamate. The activity of this receptor is mediated by a G-protein that activates a phosphatidylinositol-calcium second messenger system.

The Homer proteins form a physical tether linking mGluRs with the inositol trisphosphate receptors (IP3R) that appears to be due to the proline-rich Homer ligand (PPXXFr). Activation of PI turnover triggers intracellular calcium release . Metabotropic glutamate receptor (MGluR) function is altered in the mouse model of human Fragile X syndrome, a disorder caused by loss of function mutations in the Fragile X messenger ribonucleoprotein 1 gene Fmr1. Homer 3 (and to a lesser extent Homer 1b/c) has been shown to form a multimeric complex with mGlu1a and the IP3 receptor, indicating that Homers may play a role in the localisation of receptors to their signalling partners .
Disks large homologue 1, N-terminal PEST domain (DLG1_PEST_dom)
Type: Domain

This domain can be found in Disks large homologue 1 (DLG1 or SAP97), a membrane-associated guanylate kinase protein (MAGUK) that serves as an important determinant of localization and organisation of ion channels into specific plasma membrane domains .
Mrp/NBP35 ATP-binding protein (Mrp/NBP35_ATP-bd)
Type: Family

This entry contains cytosolic Fe-S cluster assembling factors NBP35 and CFD1. The NBP35-CFD1 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins. Nucleotide binding and hydrolysis seems to be critical for loading of Fe-S clusters onto CFD1 and NBP35 . In higher eukaryotes NBP35 and CFD1 are known as NUBP1 and NUBP2, and NUBP1 is also involved in iron regulation .

Bacterial homologues ApbC and MRP (Multiple Resistance and pH adaptation in E. coli) have been shown to contain an ATP-binding domain at the N terminus and have ATPase activity. MRP is a membrane-spanning protein and functions as a Na+/H+ antiporter . Archaeal homologues function as iron-sulfur cluster carriers .
Protein of unknown function DUF2469 (DUF2469)
Type: Family

This entry represents a group of proteins often found in Actinomycetes species, clustered with signal peptidase and/or RNAse-HII.
Spore coat protein Z/Y (Spore_coat_protein_Z/Y)
Type: Family

This entry represents proteins spore coat proteins Z (aka CotZ) and Y (aka CotY). They belong to a cysteine-rich spore coat family and are necessary for the assembly of intact exosporium.
Ionotropic glutamate receptor, L-glutamate and glycine-binding domain (Glu/Gly-bd)
Type: Domain

This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine in the ionotropic glutamate receptor NMDA . It is found in association with

.
Domain of unknown function DUF2470 (DUF2470)
Type: Domain

This entry represents an uncharacterised domain that can be found in a group of putative haem-iron utilisation proteins, such as HugZ from H. pylori and non-canonical heme oxygenase HOZ form Arabidopsis. HOZ is a dimeric β-barrel protein that binds to heme and catalyses its degradation to produce biliverdin . This domain can also be found in C-terminal of the glutamyl-tRNA reductase-binding (GluTRBP) protein from Arabidopsis . GluTRBP is involved in the regulation of glutamyl-tRNA reductase (GluTR) which is important for the synthesis and distribution of 5-aminolevulinate, a precursor in heme and chlorophyll biosynthesis . GluTRBP is necessary for efficient photosynthetic electron transport in chloroplasts .
Bacteriophage Mu, GpM, tail tube (Phage_Mu_GpM_tail_tub)
Type: Family

This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Energy-converting hydrogenase B, subunit P (Energy-convert_hydgase-B_suP)
Type: Family

Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane. This entry contains subunit P of Ehb.
Universal stress protein B (Universal_stress_protein_B)
Type: Family

Universal stress protein B (UspB) in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein. Over expression of UspB results in cell death in stationary phase, and mutants of UspB are sensitive to ethanol exposure during stationary phase .
Hemin uptake protein HemP (Hemin_uptake_protein_HemP)
Type: Family

This entry represents bacterial proteins that are involved in the uptake of the iron source hemin .
Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain (Oxoglutarate/Fe-dep_Oase_C)
Type: Domain

This entry represents the C-terminal degradation domain of oxoglutarate and iron-dependent oxygenase (Ofd1), the domain being conserved from yeasts to humans.

Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N (the N-terminal transcription factor domain of Sre1) in the presence of oxygen . Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts .
mRNA capping enzyme catalytic subunit, RNA triphosphatase domain, virus (MCEL_TPase)
Type: Domain

mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (

) . The N-terminal module comprises a TPase domain, represented in this entry, followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase,

) and OB fold (

) domains . This domain catalyses the hydrolysis of the the 5' triphosphate end of the pre-mRNA.
Mitochondrial outer membrane translocase complex, subunit Tom5 (Tom5)
Type: Family

This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore . Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Photosystem P840 reaction-centre, cytochrome c-551 (Cytochrome-c551)
Type: Family

A photosynthetic reaction-centre complex is found in certain green sulphur bacteria such as Chlorobium vibrioforme, which are anaerobic photo-auto-trophic organisms. The primary electron donor is P840, a probable B-Chl a dimer, and the primary electron acceptor is a B-Chl monomer. On the donor side, c-type cytochromes are known to function as electron donors to photo-oxidised P840 .

This entry represents a cytochrome c551 component of the PRC. It is a membrane-bound cytochrome containing a single haem group.
Misato Segment II tubulin-like domain (Misato_II_tubulin-like)
Type: Domain

The misato protein contains three distinct, conserved domains, segments I, II and III and is involved in the regulation of mitochondrial distribution and morphology . This entry represents misato segment II.

Segments I and III are common to tubulins (

), but segment II aligns with myosin heavy chain sequences from Drosophila melanogaster (Fruit fly,

), rabbit (

), and human.
GerMN domain (GerMN)
Type: Domain

The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel α-β fold.
Putative zinc-finger domain (Putative_zinc-finger_domain)
Type: Domain

This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Photosystem I P840 reaction centre protein PscD (PSI_P840_PscD)
Type: Family

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin .
Trypanosome variant surface glycoprotein, C-terminal (Variant_surf_glycoprt_trypan_C)
Type: Domain

This entry represents the C-terminal of the variant surface glycoprotein. The trypanosome parasite expresses these proteins to evade the immune response . The variant surface glycoprotein (VSG) of Trypanosoma brucei forms a coat on the surface of the parasite; by the expression of a series of antigenically distinct VSGs in the surface coat the parasite escapes the host immune response.
Iron sulphur domain-containing, mitoNEET, N-terminal (FeS-contain_mitoNEET_N)
Type: Domain

The CDGSH iron sulphur domain are a group of iron-sulphur (Fe-S) clusters and a unique 39 amino acid CDGSH domain [C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H].
Minor capsid protein, putative (Minor_capsid_put)
Type: Family

This entry represents a putative minor capsid (or tail-knob) protein from a number of bacteriophages.
Protein of unknown function DUF4198 (DUF4198)
Type: Family

This family, which includes Haemophilus influenzae protein HI_1624, is functionally uncharacterised. Some family members were previously annotated as prokaryotic transmembrane nickel uptake transporters, NikM. This has been shown to be incorrect, as the proteins matched do not exhibit transmembrane properties, nor do they contain conserved residues associated with NikM proteins .
S-adenosylmethionine-dependent methyltransferase (SAM-dep_methyl-trfase)
Type: Domain

Members of this entry are S-adenosylmethionine-dependent methyltransferases from gammaproteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyse the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalysed by the S-adenosylmethionine-dependent methyltransferases. SAM (S-adenosylmethionine, also known as AdoMet) is well known as the methyl donor for the majority of methyltransferases that modify DNA, RNA, histones and other proteins, dictating replicational, transcriptional and translational fidelity, mismatch repair, chromatin modelling, epigenetic modifications and imprinting .
Protein of unknown function DUF2487 (DUF2487)
Type: Family

This entry represents proteins with unknown function that appears to be restricted to Bacillus sp.
Ycf54 protein (Ycf54)
Type: Family

Ycf54 is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. Ycf54 is a component of the MgPME-cyclase complex. Ycf54 plays two roles in the function of the MgPME-cyclase. First, it plays a critical role in t assembly/stability of the Mg-cyclase complex and its constituents and, secondly, is required for normal Pchlide formation. Both functions indicate that this protein is required for optimal MgPME-cyclase activity, although it is not absolutely essential .
Domain of unknown function DUF2489 (DUF2489)
Type: Domain

This entry represents bacterial uncharacterised proteins.
Spore germination protein GerPA/GerPF (Spore_germination_GerPA)
Type: Family

This is a bacterial family of proteins that are required for the formation of functionally normal spores. Proteins in this family may be involved in establishing normal coat structure and/or permeability which could control the access of germinants to their receptor .
Protein of unknown function DUF2490 (DUF2490)
Type: Family

This entry represents a bacterial family of uncharacterised proteins.
Putative metal-binding protein (Metal-bd_prot_put)
Type: Family

This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Protein of unknown function DUF2491 (DUF2491)
Type: Family

This entry represents a family of bacterial uncharacterised proteins, including YjfK (

) from Escherichia coli.
Rrn9 domain (Rrn9_dom)
Type: Domain

This entry represent a domain found in the Rrn9 protein, a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. This domain seems to be constrained to fungi, is the two highly conserved regions of proteins which form one of the subunits of UAF and appears to be the region responsible for the interaction with TBP, a TATA-binding transcription initiation factor protein .
Protein Rot1 (Rot1)
Type: Family

Rot1 is a molecular chaperone involved in protein folding in ER . It is required for normal levels of the cell wall 1,6-beta-glucan and for protein N- and O-glycosylation . It also controls actin cytoskeleton polarization to the mother-bud neck and CLB2 protein stability .
Herpesvirus UL40 (Herpes_UL40)
Type: Family

This entry represents glycoprotein UL40 from Human cytomegalovirus (HHV-5) (Human herpesvirus 5). HHV-5 has evolved mechanisms to interfere with a host's immune recognition, including targeting antigen presentation by MHC class I molecules. The signal sequence of the HHV-5 encoded UL40 polypeptide contains an HLA-E ligand identical with HLA-Cw*0304. The first 37 residues of UL40, including this ligand, are predicted to encode a signal peptide. The virus thus prevents the lysis by NK (natural killer) cells of the cell it has invaded .
Biofilm-dependent modulation protein Bdm, putative (Biofilm-dep_modulation_Bdm_put)
Type: Family

This entry represents a group of tightly conserved proteins from Enterobacteriaceae which are annotated as being biofilm-dependent modulation protein homologues. This entry includes Bdm, whose expression is reduced in biofilms and is repressed by a high salt concentration .
Stress-induced protein, KGG, repeat (Stress-induced_KGG_rpt)
Type: Repeat

This repeat contains a highly conserved, characteristic sequence motif, KGG, that is recognised by plants and lower eukaryotes.

Further downstream from this motif is a Walker A, nucleotide binding motif. YciG is expressed as part of a three-gene operon, yciGFE and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress .
YspA, cpYpsA-related SLOG (YAcAr)
Type: Domain

These proteins are related to the SLOG superfamily and show associations with NAD utilisation and ADP-ribosylation domains including NUDIX, NADAR and MACRO. They are predicted to function as sensors of nucleotides, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors. Also associates in a distinct system with a phosphoribosyltransferase (PRTase) domain .
Uncharacterised protein family HI1736/YgjV (Uncharacterised_HI1736/YgjV)
Type: Family

This entry represents inner membrane proteins, including the uncharacterised HI_1736 and YgjV proteins. Their function is unknown.
Protein of unknown function DUF2496, YbaM-related (DUF2496_YbaM-rel)
Type: Family

This family consists of proteins from Gammaproteobacteria species. Many members are annotated as being like the Escherichia coli protein; YbaM.
Myticin preproprotein (Myticin_preproprotein)
Type: Family

Myticin is a cysteine-rich peptide produced in three isoforms, A, B and C, by Mytilus galloprovincialis (Mediterranean mussel). Isoforms A and B show antibacterial activity against Gram-positive bacteria, while isoform B is additionally active against the fungus Fusarium oxysporum and a Gram-negative bacterium, Escherichia coli (streptomycin resistant strain D31) . Myticin-prepro is the precursor peptide. The mature molecule, named myticin, consists of 40 residues, with four intramolecular disulphide bridges and a cysteine array in the primary structure different from that of previously characterised cysteine-rich antimicrobial peptides. The first 20 amino acids are a putative signal peptide, and the antimicrobial peptide sequence is a 36-residue C-terminal extension. Such a structure suggests that myticins are synthesised as prepro-proteins that are then processed by various proteolytic events before storage in the haemocytes as the active peptide. Myticin precursors are expressed mainly in the haemocytes.
Protein of unknown function DUF2497 (DUF2497)
Type: Family

Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Protein of unknown function DUF2498 (DUF2498)
Type: Family

This entry represents proteins found in gammaproteobacteria, including YciN from Escherichia coli. Their function is not known.
Uncharacterised protein family Ycf49 (Uncharacterised_Ycf49)
Type: Family

This entry represents proteins found in plants, lower eukaryotes, and bacteria and the chloroplast where it is annotated as Ycf49 or Ycf49-like. The function is not known though several members are annotated as putative membrane proteins. As the family is primarily found in phototrophic organisms it may play a role in photosynthesis.
Protein of unknown function DUF2500 (DUF2500)
Type: Family

This entry represents a group of proteins that is largely confined to the Gammaproteobacteria. The function is not known.
Protein of unknown function DUF2501 (DUF2501)
Type: Family

This entry represents proteins that are found in Proteobacteria. Several are annotated as being YjjA or YjjA-like, but this protein is uncharacterised.
Protein of unknown function DUF2502 (DUF2502)
Type: Family

This entry represents proteins mainly found in Gammaproteobacteria. The function is not known.
Protein of unknown function DUF2505 (DUF2505)
Type: Family

This entry represents proteins found Actinobacteria and Proteobacteria. The function is not known.
Protein of unknown function DUF2507 (DUF2507)
Type: Family

This entry represents a family of conserved proteins found primarily in Firmicutes. The function is not known.
Protein of unknown function DUF2508 (DUF2508)
Type: Family

This entry represents a protein family of unknown function that is conserved in the firmicutes.
Uncharacterised protein family Ycf15 (Uncharacterised_Ycf15)
Type: Family

In some species of plants the ycf15 gene is probably not a protein-coding gene because the protein in these species has premature stop codons. Most of the members of the family are hypothetical or uncharacterised .
Aminoglycoside-2''-adenylyltransferase (Aminoglyc_AdlTrfase)
Type: Family

Aminoglycoside-2''-adenylyltransferase is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin . The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents .
PhoP regulatory network protein YrbL (PhoP_reg_network_YrbL)
Type: Family

This entry represents proteins that are activated by the protein PhoP. PhoP controls the expression of a large number of genes that mediate adaptation to low Mg2+ environments and/or virulence in several bacterial species. YbrL is proposed to be acting in a loop activity with PhoP and PrmA analogous to the multi-component loop in Salmonella sp., where the PhoP-dependent PmrD protein activates the regulatory protein PmrA, and the activated PmrA then represses transcription from the PmrD promoter which harbours binding sites for both the PhoP and PmrA proteins. Expression of YrbL is induced in low Mg2+ in a PhoP-dependent fashion and repressed by Fe3+ in a PmrA-dependent manner .