SII-SWORD/CoKE huggingface dataset:
Competence, DNA-entry nuclease inhibitor, ComJ (Competence_nuclease_inhibitor)
Type: Family

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

The proteins in this entry play a role in the competence of cells to be transformed. They inhibit the activity of the DNA-entry nuclease. DNA-entry nuclease inhibitor is a subunit of a 75kDa protein complex, which governs binding and entry of donor DNA. The complex is a tetramer of two subunits of the DNA-entry nuclease and two subunits of a competence-specific protein ComJ. Only the complex is able to bind ds- and ss-DNA . It is found in the plasma membrane.
Uncharacterised protein family YhcU (Uncharacterised_YhcU)
Type: Family

This entry contains proteins with no known function.
Poxvirus T3C (Poxvirus_T3C)
Type: Family

This entry contains proteins with no known function.
Transcription regulator CaiF/GrlA (Tscrpt_reg_CaiF/GrlA)
Type: Family

This is a family of transcriptional regulators that includes CaiF and GrlA. CaiF is a specific carnitine-sensitive transcription regulator . CaiF and CRP, a cyclic AMP receptor protein, are required to activate the cai and fix operons, which are involved in anaerobic carnitine metabolism . GrlA is encoded within the LEE type III secretion system in the enteropathogenic E. coli O157:H . GrlR interacts with GrlA at its Helix-Turn-Helix (HTH) motif, preventing GrlA from binding to its target promoter DNA.
Biofilm regulator BssR (Biofilm_regulator_BssR)
Type: Family

This entry represents Biofilm regulator, BssR (from the gene also known as yliH). It represses Escherichia coli biofilm formation in M9C glu and LB glu media but not in M9C and LB media. It may act as a global regulator of several genes involved in catabolite repression and stress response and regulation of the uptake and export of signalling pathways. It could also be involved the regulation of indole as well as uptake and export of AI-2 through a cAMP-dependent pathway .
Uncharacterised protein family alr2393 (Uncharacterised_alr2393)
Type: Family

This entry contains proteins with no known function.
Tail accessory factor GP4 (Tail_accessory_Gp4)
Type: Family

The tail complex in bacteriophage P22, and related phages, mediates host cell attachment and DNA injection. Tail assembly is a complex event that is essential for the retention and stabilisation of the newly packaged DNA within the capsid. This process involves the sequential addition of three tail accessory factors (GP4, GP10, GP26) and the adhesion tailspike protein (GP9) to the capsid-bound portal protein .

Gp4 is the first factor to attach after DNA packaging. Twelve monomeric subunits of GP4 bind to the exposed surface of the portal ring, beginning the tail assembly process. GP4 does not physically block the DNA entry/exit channel, but appears to act as a structural adaptor for the other tail accessory factors GP10 and GP26 .

Gp4 has been shown to have peptidoglycan hydrolase activity .
Uncharacterised protein family YbgS (Uncharacterised_YbgS)
Type: Family

This entry contains proteins with no known function.
INO80 complex subunit Ies5 (Ies5)
Type: Family

This entry represents the INO80 subunit 5 or Ies5, which has been shown to associate with the INO80 chromatin-remodelling complex under low-salt conditions , though its function is unknown.

The INO80 complex is involved in chromatin-remodelling by promoting the repositioning (sliding) or eviction of nucleosomes from the DNA in an ATP-dependent process. The INO80 chromatin-remodelling complex of Saccharomyces cerevisiae (Baker's yeast) is composed of at least 15 subunits and has a molecular mass of about 1.2 to 1.5 MDa. In S. cerevisiae the core conserved subunits are:

ATPase; Ino80.

RuvB-like; Rvb1 and Rvb2.

Actin; Act1.

Actin-related: Arp4, Arp5 and Arp8.

YEATS protein ; Taf14.

The non-conserved subunits are: Ies1, Ies2, Ies3, Ies4, Ies5, Ies6 and Nhp10 .
Host transcription inhibitor Alc (Host_transcript_inhib_Alc)
Type: Family

Bacteriophage T4 infection rapidly shuts down transcription in the host cell and any other phages that may be present. This is accomplished by specifically blocking transcription of cytosine-containing DNA. T4 is protected from this as its DNA contains a substituted base, hydroxymethylcytosine, in place of the usual cytosine. The Alc protein plays a key role in this process by unfolding the host genome and blocking transcription of cytosine-containing DNA .
Uncharacterised protein family YbjM (Uncharacterised_YbjM)
Type: Family

This entry contains membrane proteins with no known function.
Mobilisation protein B (Mobilisation_protein_B)
Type: Family

Mobilization protein B (MobB) contains a putative membrane-spanning domain, and might be involved in anchoring or presenting MobA, and the covalently-linked plasmid DNA, to the conjugative pore for subsequent export. In agreement with this, MobB has been shown to be associated with the membrane. Deletion of the membrane-spanning domain disrupts this association and decreases the frequency of both type IV transport and plasmid mobilization. MobB is one out of three proteins encoded by RSF1010 that are required for its mobilization along with MobA and MobC . MobB encoded by the broad-host-range plasmid R1162 is required for its efficient transfer by conjugation. The C-terminal half of the protein contains a membrane domain essential for transfer, while the other, functionally active region of MobB, identified by mutagenesis, is at the N-terminal end. One mutation affecting this region inhibits replication, suggesting that this part of the protein is contacting and sequestering the relaxase-linked primase. A model that represents MobB molecules as anchored in the membrane at one end and engaging the relaxase at the other. This arrangement is suggested to increase the transfer frequency by raising the probability of contact between the relaxase and the membrane-embedded, coupling protein for type IV secretion .
Protein of unknown function DUF5504 (DUF5504)
Type: Family

This is a family of unknown function found in Lactobacillus. Family members have 4 predicted trans-membrane regions.
Competence operon G protein 7, ComGG (Competence_ComGG)
Type: Family

This entry represents comG operon protein 7, ComGG. It is required for DNA-binding during transformation of competent bacterial cells . About half of pre-ComGG is present as a peripheral membrane protein and the other half as an integral protein. Upon partial processing, ComGG is translocated to a position outside the membrane .

The comG operon of Bacillus subtilis encodes seven membrane associated proteins which function in binding of transforming DNA to the competent cell surface . ComGC, GD, GE and GG have N-terminal sequence motifs typical of type 4 pre-pilins and are processed by a pathway that requires the product of comC, also an essential competence gene. They form pilin-like structures that are localised to the cytoplasmic membrane and cell wall . The comG operon also consist of ComGF, a small integral membrane protein, ComGA and ComGB, which are predicted to be a nucleotide binding protein and an integral membrane protein respectively . When strains missing each of the 7 proteins are created, they were all found to be nontransformable and failed to bind transforming DNA to the cell surface .

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .
Alpha-ketoglutarate dehydrogenase component 4/YMR-31 (Kgd4/YMR-31)
Type: Family

This entry represents the alpha-ketoglutarate dehydrogenase component 4 (Kgd4, also referred to as Ymr31/MRPS36) which was originally identified as a subunit of the mitochondrial ribosome. Through biochemical studies, it was shown that this protein co purifies with the oxoglutarate dehydrogenase complex (OGDC), also called alpha-ketoglutarate dehydrogenase complex (KGDH). Both mitochondrial ribosome 28S subunit and OGDC have a similar size and OGDC is highly abundant, being found to contaminate ribosomal preparations performed by sequential centrifugation steps . Kgd4 plays an evolutionarily conserved role in the organization of mitochondrial α-KGDH complexes of fungi and animals which constitutes a molecular adaptor that is necessary to form a stable α-KGDH enzyme complex .
Uncharacterised protein family F46C5.1 (Uncharacterised_F46C5.1)
Type: Family

This entry contains membrane proteins with no known function.
Uncharacterised protein family LpqV (Uncharacterised_LpqV)
Type: Family

This entry contains putative lipoproteins proteins with no known function.
Protein of unknown function DUF4186 (DUF4186)
Type: Family

This protein family is functionally uncharacterised.
Protein of unknown function DUF5448 (DUF5448)
Type: Family

This is a family of unknown function found in Gammaproteobacteria.
Uncharacterised protein family MJ1658 (Uncharacterised_MJ1658)
Type: Family

This entry contains proteins with no known function.
Androgenic gland hormone (AGH)
Type: Family

This family contains members such as the androgenic gland hormone (AGH) of the woodlouse, Armadillidium vulgare. AGH is a heterodimeric glycopeptide synthesized and secreted from androgenic glands. It is responsible for sex differentiation in crustaceans and contains 4 disulfide bonds .
MinK-related peptide, potassium channel accessory subunit protein 4 (MPS4)
Type: Family

This entry represents MinK-related peptide, potassium channel accessory subunit protein 4 from Caenorhabditis elegans (MPS4) and similar proteins found in nematodes. MinK-related peptides (MiRPs or KCNEs) are single-transmembrane proteins that associate with pore-forming ion-channel sub-units to form stable complexes with channel properties markedly distinct from those of the isolated pore-forming sub-units . MPS4 is expressed exclusively in the C. elegans nervous system and is essential for neuronal excitability .
Uncharacterised protein family YehE (Uncharacterised_YehE)
Type: Family

This entry contains proteins with no known function.
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf112 (AcMNPV_Orf112)
Type: Family

This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf112; it is a family of uncharacterised viral proteins.

This entry also represents the N-terminal region of Fowlpox virus (FPV) FPV217. The protein family is uncharacterised.
Uncharacterised protein family YqhV (Uncharacterised_YqhV)
Type: Family

This bacterial family of proteins has no known function. This family includes the B. subtilis YqhV protein which is found just upstream of the SpoIIIA operon, suggesting it may play a role in sporulation or its regulation [1]. The protein is composed of three hydrophobic α-helices that may form transmembrane helices .
Pancreatic hormone-like, conserved site (Pancreatic_hormone-like_CS)
Type: Conserved_site

This entry represents a conserved region corresponding to the C-terminal end of the active peptide.

This entry represents a group of animal proteins, including Pancreatic hormone , also known as Pancreatic polypeptide is a peptide (PP), which is synthesized in pancreatic islets of Langherhans and acts as a regulator of pancreatic and gastrointestinal functions.

The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length and has an amidated C terminus . The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a β-turn, and 14-32 an α-helix, held close to the first helix by hydrophobic interactions . Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution . Both N- and C- terminal ends are required for activity: receptor binding and activation functions may reside in the N and C termini respectively .

Pancreatic hormone is part of a wider family of active peptides that includes:

Neuropeptide Y (NPY or melanostatin) , one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotropin-releasing hormone.

Peptide YY (PYY) . PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictor action and inhibits jejunal and colonic mobility. Known as goannatyrotoxin-Vere1 in the venom of the pygmy desert monitor lizard (Varanus eremius) where it has a triphasic action: rapid biphasic hypertension followed by prolonged hypotension in prey animals .

Various NPY and PYY-like polypeptides from fish and amphibians .

Neuropeptide F (NPF) from invertebrates such as worms and snail.

Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity.

Polypeptide MY (peptide methionine-tyrosine). A regulatory peptide from the intestine of the sea lamprey (Petromyzon marinus) .

All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesised as larger protein precursors.
Uncharacterised protein family YusU (Uncharacterised_YusU)
Type: Family

This entry contains proteins with no known function.
Uncharacterised protein family, FAM23-like, transmembrane (Uncharacterised_FAM23-like_TM)
Type: Family

This entry represents a group of uncharacterised transmembrane proteins that are members of the FAM23 family of proteins.
NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site (NADH_UbQ_OxRdtase_CS)
Type: Conserved_site

Respiratory-chain NADH dehydrogenase (

) (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 30 Kd (in mammals) which has been found to be :

Nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa.

Mitochondrial encoded in Paramecium (protein P1), and in the slime mold Dictyostelium discoideum (ORF 209).

Chloroplast encoded in various higher plants (ORF 159).

It is also present in bacteria:

In the cyanobacteria Synechocystis strain PCC 6803 (gene ndhJ).

Subunit C of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoC).

Subunit Nqo5 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase. Nqo5 composes the hydrogenase-like module together with the Nqo4, Nqo6, and Nqo9 subunits. Homologous proteins of the Nqo5 subunit are also contained in membrane-bound multisubunit hydrogenases, while soluble-type hydrogenases are not. This subunit is essential in complex I assembly .

This entry represents a conserved region found towards the C terminus of these proteins.
T-cell receptor-associated transmembrane adapter 1 (T-cell_rcpt-assoc_TM_adapter-1)
Type: Family

This entry represents T-cell receptor-associated transmembrane adapter 1. It is thought to stabilise the TCR (T-cell antigen receptor)/CD3 complex at the surface of T-cells .
Cecropin/Sarcotoxins/Aedesins (CecC/Srx/CECD)
Type: Family

This entry represents antimicrobial peptides such as Cecropins, Sarcotoxins and Aedesins from insects.

Cecropins are potent antibacterial proteins that constitute a main part of the cell-free immunity of insects. Cecropins are small proteins of about 35 amino acid residues active against both Gram-positive and Gram-negative bacteria. They seem to exert a lytic action on bacterial membranes. Cecropins have been given various names, including bactericidin, lepidopteran and sarcotoxin. All of these peptides are structurally related.
mRNA transport factor GFD1 (mRNA_transport_factor_GFD1)
Type: Family

This entry represents the mRNA transport factor GFD1. GFD1 is a coiled-coiled protein of unknown function, which was identified as a high-copy suppressor of mutant alleles of ATP-dependent RNA helicase DBP5, which is involved in mRNA export from the nucleus. It may also play an important role in a late stage of NAB2-mRNA export .
Equine arteritis virus envelope glycoprotein 5 (EAV_Gp5)
Type: Family

Arteriviruses encode four envelope proteins, GL, GS, M and N. GL envelope glycoprotein is heterogenously glycosylated with N-acetyllactosamine in a cell-type-specific manner. The GL glycoprotein expresses the neutralization determinants .

This entry is specific for the GL envelope glycoproteins from equine arteritis virus.
Protein of unknown function DUF2713 (DUF2713)
Type: Family

This entry contains proteins with no known function. In some organisms this represents the C-terminal domain of a fusion protein with YjbL.
Atypical dual specificity phosphatase, subfamily A (Atypical_DUSP_subfamA)
Type: Family

This entry represents atypical dual specificity phosphatase subfamily A.

Dual specificity phosphatases (DUSPs) are members of the superfamily of protein tyrosine phosphatases . They remove the phosphate group from both phospho-tyrosine and phospho-serine/threonine residues. They are structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR . They are characterised as VHR- or Cdc25-like .

In general, DUSPs are classified into the following subgroups :

Slingshot phosphatases

Phosphatase of regenerating liver (PRL)

Cdc14 phosphatases

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN)-like and myotubularin phosphatases

Mitogen-activated protein kinase phosphatases (MKPs)

Atypical DUSPs

The atypical DUSPs share a high degree of similarity with the MKP subgroup, but lack the N-terminal regulatory domain, which provides the substrate specificity towards the MAP kinases. These atypical-DUSPs form a heterogeneous group and have in common the presence of a single catalytic PTP domain. VHR was the first characterised member of this subfamily; its crystal structure is known .

The function of many atypical DUSPs remains unknown, although some have been related to regulation of MAP kinase pathways . VHR has also been related to the control of cell-senescence .
Epidermin biosynthesis protein EpiC (Epidermin_biosynth_EpiC)
Type: Family

The LanC-like protein superfamily encompasses a highly divergent group of peptide-modifying enzymes, including the eukaryotic and bacterial lanthionine synthetase C-like proteins (LanC) ; subtilin biosynthesis protein SpaC from Bacillus subtilis ; epidermin biosynthesis protein EpiC from Staphylococcus epidermidis ; nisin biosynthesis protein NisC from Lactococcus lactis ; GCR2 from Arabidopsis thaliana ; and many others.

The 3D structure of the lantibiotic cyclase from L. lactis has been determined by X-ray crystallography to 2.5A resolution . The globular structure is characterised by an all-α fold, in which an outer ring of helices envelops an inner toroid composed of 7 shorter, hydrophobic helices. This 7-fold hydrophobic periodicity has led several authors to claim various members of the family, including eukaryotic LanC-1 and GCR2, to be novel G protein-coupled receptors ; some of these claims have since been corrected .

The EpiC protein from S. epidermidis, a hydrophobic but nevertheless soluble protein, is involved in the biosynthesis of the lantibiotic epidermin . Its molecular structure is stabilised by a number of intramolecular disulphide bridges; the cysteine residues within its WCYG and CHG motifs, highly conserved in LanC-like proteins , lie on 2 of the inner helices.
Nerve growth factor-like (Nerve_growth_factor-like)
Type: Family

During the development of the vertebrate nervous system, many neurons become redundant (because they have died, failed to connect to target cells, etc.) and are eliminated. At the same time, developing neurons send out axon outgrowths that contact their target cells . Such cells control their degree of innervation (the number of axon connections) by the secretion of various specific neurotrophic factors that are essential for neuron survival. One of these is nerve growth factor (NGF or beta-NGF), a vertebrate protein that stimulates division and differentiation of sympathetic and embryonic sensory neurons . NGF is mostly found outside the central nervous system (CNS), but slight traces have been detected in adult CNS tissues, although a physiological role for this is unknown ; it has also been found in several snake venoms .

NGF is a protein of about 120 residues that is cleaved from a larger precursor molecule. It contains six cysteines all involved in intrachain disulphide bonds. A schematic representation of the structure of NGF is shown below:

+------------------------+
| |
| |
xxxxxxCxxxxxxxxxxxxxxxxxxxxxCxxxxCxxxxxCxxxxxxxxxxxxxCxCxxxx
| | | |
+--------------------------|-----+ |
+---------------------+

'C': conserved cysteine involved in a disulphide bond.

This entry also contains NGF-related proteins such as neutrophin 3, which promotes the survival of visceral and proprioceptive sensory neurons, and brain-derived neurotrophin, which promotes the survival of neuronal populations that are located either in the central nervous system or directly connected to it .
Interleukin-15, fish (IL-15_fish)
Type: Family

Interleukins (IL) are a group of cytokines that play an important role in the immune system. They modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells.

Interleukin-15 (IL-15) has a variety of biological functions, including stimulation and maintenance of cellular immune responses . It is required for division of CD8+ T cells of memory phenotype, a process that is increased by inhibition of IL-2 . The numbers of CD8+ memory T cells in animals may, therefore, be controlled by a balance between IL-15 and -2.

IL-15 has been identified in mammals, birds and fish. Recombinant fish IL-15 has been shown to stimulate splenic leukocytes, inducing a large increase in the expression of the antiviral, immunoregulatory cytokine, interferon-gamma .This entry represents interleukin-15 found in fish.