This family consists of several hypothetical Enterobacterial proteins of around 100 residues in length. Members of this family are often described as YbjC. In Escherichia coli the ybjC gene is located downstream of nfsA (which encodes the major oxygen-insensitive nitroreductase). It is thought that nfsA and ybjC form an operon an its promoter is a class I SoxS-dependent promoter [
]. The function of this family is unknown.
Intermembrane transport protein PqiA-like, Enterobacteria-type
Type:
Family
Description:
This family consists mainly of proteins from Enterobacteria, and includes intermembrane transport proteins PqiA and YebS, which are components of transport pathways that contribute to membrane integrity [
]. The promoter for the pqiA gene is inducible by paraquat, a superoxide radical-generating agent, and other known superoxide generators [].
This family includes bacterial colicin and pyocin immunity proteins [
,
]. These immunity proteins can bind specifically to the DNase-type colicins and pyocins and inhibit their bactericidal activity. The 1.8-angstrom crystal structure of the ImmE7 protein consists of four antiparallel α-helices []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. Pyocin protects a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin E2; it is thus essential both for autonomous replication and colicin E2 immunity [].
This entry represents the UPF0234 family of uncharacterised proteins, which includes YajQ.In Pseudomonas syringae, YajQ functions as a host protein involved in the temporal control of bacteriophage Phi6 gene transcription. It has been shown to bind to the phage's major structural core protein P1, most likely activating transcription by acting indirectly on the RNA polymerase. YajQ may remain bound to the phage particles throughout the infection period [
,
]. Earlier, YajQ was characterized as a putative nucleic acid-binding protein based on the similarity of its (ferredoxin-like) three-dimensional topology with that of RNP-like RNA-binding domains [,
].
This domain is found in members of the ABC type 3 transporter family [
]. Proteins containing this domain include: Cell division protein FtsX from Gram-negative and Gram-positive bacteria. It is a component of the septal ring [
]. It may insert division proteins into the cytoplasmic membrane []. Permease protein MacB 1. It is part of the tripartite efflux system MacAB-TolC [
]. Lipoprotein-releasing system transmembrane protein LolC. It is part of an ATP-dependent transport system LolCDE responsible for the release of lipoproteins targeted to the outer membrane from the inner membrane [
]. Putative hemin transport system permease protein HrtB. It may be Part of the ABC transporter complex hrt involved in hemin import [
]. Bacitracin export permease protein BceB. It is art of the ABC transporter complex BceAB (TC 3.A.1.123.5) involved in bacitracin export [
].ABC transporter permease YtrF. It is part of the ABC transporter complex YtrBCDEF that plays a role in acetoin utilization during stationary phase and sporulation [
].ABC transporter permease protein YxdM. It is part of the ABC transporter complex YxdLM which could be involved in peptide resistance [
].
This entry represents ZapA, an activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. ZapA is recruited early at mid-cell but it is not essential for cell division.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [
,
]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae.
FliK controls the length of the flagellar hook. It detects when the flagellar hook substructure has reached its optimal length. Then, it terminates hook export and assembly and transmits a signal to begin filament export, the final stage in flagellar biosynthesis. The exact mechanism of how FliK achieves this is not known [
,
]. FliK is a two-domain protein with the central portion of the sequence acting as a hinge or connector between the two [].
The CcsA protein family represents one of two essential proteins in system II c-type cytochrome biogenesis [
]. Additional proteins tend to be part of the system but can often be replaced by chemical reductants such as dithiothreitol. These proteins are often named CcsB in Bordetella and some other bacteria, ResC in Bacillus (where there is additional N-terminal sequence), while chloroplast proteins are consistently named CcsA.
This domain occurs at the N terminus of Afi1 (Arf3-interacting protein 1), a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3. Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity [
]. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalisation. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.
IQ calmodulin-binding motif-containing protein 1 (IQCB1, also called NPHP5) is involved in ciliogenesis [
]. Mutations in IQCB1 gene cause Senior-Loken syndrome 5 (SLSN5), which is a renal-retinal disorder characterised by progressive wasting of the filtering unit of the kidney (nephronophthisis), with or without medullary cystic renal disease, and progressive eye disease [].
ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [
].The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [,
,
].The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly β-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel β-sheet of armI by a two-fold axis [,
,
,
,
,
].The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [
]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [,
]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [,
,
].This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase.
ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [].The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [,
,
].The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly β-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel β-sheet of armI by a two-fold axis [
,
,
,
,
,
].The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [
]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [,
]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [,
,
].This entry represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families.
Uncharacterised conserved protein UCP021697, membrane
Type:
Family
Description:
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
This family of proteins is functionally uncharacterised and it is predominantly found in bacteria and archaea. This family has some overlaps with families from the clan CL0034.
TraF protein undergoes proteolytic processing associated with export. The 19 amino acids at the amino terminus of the polypeptides appear to constitute a typical membrane leader peptide - not included in this family, while the remainder of the molecule is predicted to be primarily hydrophilic in character [
]. F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer, and they are both localised to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor [].TrbB is closely related to TraF which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase. TrbB may be involved in pilin assembly [
].
This entry includes TRAP transporters that binds to ketoacids such as pyruvate and alpha-ketobutyrate, xylulose, and other unknown ligands [
,
,
]. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap [].
Uncharacterised conserved protein UCP019883, membrane
Type:
Family
Description:
There is currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain transmembrane segments.
Uncharacterised conserved protein UCP019464, methanogenesis
Type:
Family
Description:
There is currently no experimental data for members of this group or their homologues. Based on distant sequence similarity, they may be tentatively predicted to be nucleic acid-binding proteins, they are also likely to be linked to methanogenesis or a process closely connected to it.
CATSPER (cationic channel of sperm) is a complex ion channel that mediates Ca2+ entry in sperm flagellum and is required for sperm hyperactivation and male fertility [
]. The CATSPER channel consists of four CatSper proteins (CatSper1-4) that form a tetramer surrounding a Ca(2+)-selective pore. In addition to the pore-forming proteins, the CATSPER channel contains auxiliary subunits [].All four CatSper proteins are predicted to contain a common coiled-coil protein-protein interaction domain in their C-terminal tail [
] and all four are required for male fertility and sperm cell hyperactivated motility []. The CatSper channel of human sperm is activated by progesterone [].This entry represents cation channel sperm-associated protein 4 (CatSper4) [
].
CATSPER (cationic channel of sperm) is a complex ion channel that mediates Ca2+ entry in sperm flagellum and is required for sperm hyperactivation and male fertility [
]. The CATSPER channel consists of four CatSper proteins (CatSper1-4) that form a tetramer surrounding a Ca(2+)-selective pore. In addition to the pore-forming proteins, the CATSPER channel contains auxiliary subunits [].All four CatSper proteins are predicted to contain a common coiled-coil protein-protein interaction domain in their C-terminal tail [
] and all four are required for male fertility and sperm cell hyperactivated motility []. The CatSper channel of human sperm is activated by progesterone [].This entry represents cation channel sperm-associated protein 1 (CatSper1) [
].
CATSPER (cationic channel of sperm) is a complex ion channel that mediates Ca2+ entry in sperm flagellum and is required for sperm hyperactivation and male fertility [
]. The CATSPER channel consists of four CatSper proteins (CatSper1-4) that form a tetramer surrounding a Ca(2+)-selective pore. In addition to the pore-forming proteins, the CATSPER channel contains auxiliary subunits [].All four CatSper proteins are predicted to contain a common coiled-coil protein-protein interaction domain in their C-terminal tail [
] and all four are required for male fertility and sperm cell hyperactivated motility []. The CatSper channel of human sperm is activated by progesterone [].This entry represents cation channel sperm-associated protein 2 (CatSper2) [
].
The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases [
,
].
The fliL operon of Escherichia coli contains seven genes (including fliO, fliP, fliQ and fliR) involved in the biosynthesis and functioning of the flagellar organelle [
]. The fliO, fliP, fliQ and fliR genes encode highly hydrophobic polypeptides. The fliQ gene product, a small integral membrane protein that contains two putative transmembrane (TM) regions, is required for the assembly of the rivet at the earliest stage of flagellar biosynthesis.Proteins sharing an evolutionary relationship with FliQ have been found in a range of bacteria: these include Yop translocation protein S from Yersinia pestis [
]; surface antigen-presentation protein SpaQ from Salmonella typhimurium and Shigella flexneri []; and probable translocation protein Y4YM from Rhizobium sp. (strain NGR234) []. All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [].
This is one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems, and is represented by HrpO [
]. This family is homologous to, but separate from, the flagellar biosynthetic protein FliQ.
This entry represents TPC2. It modulates neural differentiation of mouse embryonic stem cells [
]. It may also be involved in smooth muscle contraction []. Two-pore segment channels (TPCs or TPCNs) are located in membranes of acidic intracellular organelles (such as endo-lysosomes and plant vacuoles) and contain two putative pore-forming repeats. Each of these repeats contains six transmembrane segments and an intervening pore-loop, an architecture featured in voltage-gated channels [
]. Functional TPC channels are assembled from two TPC protein subunits forming a pore that conducts mainly Ca2 and Na. TPCs exist as three isoforms (TPC1-3): TPC1 and TPC2 are the most universal isoforms since TPC3 is absent from the genomes of many animals including those of human, mice, rats and flies [].
The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer [
]. TrbG is a homologue of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin, ) as well as the vir system VirB9 protein [
,
].
The VirB9 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in a type IV secretion system [
]. VirB9 is a homologue of the F-type conjugative transfer system TraK protein (which is believed to be an outer membrane pore-forming secretin, ) as well as the Ti system TrbG protein [
].
Baculoviral IAP repeat-containing protein 1 or neuronal apoptosis inhibitory protein (NAIP) is an anti-apoptotic protein which acts by inhibiting the activities of CASP3, CASP7 and CASP9. NAIP contains three baculoviral IAP repeat (BIR) domains at the amino-terminal region and a ATP/GTP binding site [
]. NAIP has been shown to inhibit apoptosis in neurons [] and in several mammalian cell lines [].
AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage [
]. More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of alphaproteobacterial types.
Fanconi anemia complementation group I (FANCI) protein is a component of the Fanconi anemia DNA damage-response pathway [
]. The protein directly binds to a variety of DNA substrates [] and plays an essential role in the repair of DNA double-strand breaks by homologous recombination. It is also involved in the repair of interstrand DNA cross-links (ICLs) by promoting FANCD2 monoubiquitination by FANCL [].Defects in the FANCI gene are a cause of Fanconi anemia complementation group I [
] - a disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair.
Mirror-image polydactyly of hands and feet (MIP) is a very rare congenital anomaly characterised by mirror-image duplication of digits. A chromosomal aberration involving mirror-image polydactyly gene 1 (MIPOL1) suggests this to be a good candidate gene for the MIP type of anomaly [
]. This entry represents the MIPOL1 protein.
Junctional sarcoplasmic reticulum protein 1 (JSRP1, also known as JP-45) may regulate voltage-sensitive calcium channel CACNA1S membrane targeting and activity [
]. The protein may also have a role in the development or maintenance of skeletal muscle strength [].
Protein CHLORORESPIRATORY REDUCTION 7-like superfamily
Type:
Homologous_superfamily
Description:
This entry includes protein from blue-green algae and plants, including CRR7 (Chlororespiratory reduction 7) protein from Arabidopsis. CRR7 is part of the chloroplastic NAD(P)H dehydrogenase complex (NDH Complex) involved in respiration, photosystem I (PSI) cyclic electron transport and CO2 uptake [
]. It is essential for the stable formation of the NDH Complex [].
Small outer capsid protein stabilises T4 capsids after the majority of the capsid assembly stages, and helps to stabilise T4 against high temperatures and pH extremes by binding the capsid surface at interfaces between Gp23 hexameric capsomers [
]. This superfamily consists of 2 alpha helices and 6 beta strands [
].
This entry represents the stage III sporulation protein AE, which is encoded in a spore formation operon spoIIIAABCDEFGH under the control of sigma G [
]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
This entry represents the stage III sporulation protein AG, which is encoded in a spore formation operon: spoIIIAABCDEFGH under the control of sigma G [
]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
This entry represents the stage II sporulation protein M, which is encoded in a spore formation operon [
]. SpoIIM is one of the three genes (spoIID, spoIIM and spoIIP, [,
,
]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
This entry represents a group of predicted integral membrane proteins, including Stage II sporulation protein M (spoIIM) from Bacillus subtilis (
).
SpoIIM is on e of four stage II sporulation proteins that is necessary for the forespore inside the mother-cell to be properly internalised through the breakdown of peptidoglycans trapped between the membranes of the septum separating the forespore and the mother-cell. The four proteins working in sequence are SpoIIB, SpoIIM, SpoIIP and SpoIID. D, M and P are in a complex with each other and the complex assembles in a hierarchical manner such that M, which serves as a membrane anchor, recruits P to the septum and P, in turn, recruits D to the septum [
].
This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation [
]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
This domain is found at the N terminus of gene product 138 (gp138) in bacteriophage phi92. Gp138 is thought to be involved in the process of opening the host cell membrane during infection. The domain has an OB-fold with an intramolecular disulfide bond between C114 and C120 [
].
Uncharacterised conserved protein UCP014897, archaea
Type:
Family
Description:
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Sec-independent protein translocase TatC, archaeal
Type:
Family
Description:
This entry represents the TatC translocase component of the Sec-independent protein translocation system in archaeal species. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane [
].
Escherichia coli RimK adds additional Glu residues to the native Glu-Glu C terminus of ribosomal protein S6. Mutation of the Glu-Glu terminus to Lys-Glu blocked addition. S6 has the C-terminal sequence Glu-Glu in few species, suggesting the homologue of rimK may have a function other than S6 modification in those species. However, most species having a member of this protein subfamily do not have an S6 homologue ending in Glu-Glu.
Target of Myb1 (TOM1)-like 2 (TOM1L2) has a probable role in protein transport [
]. It acts as a negative regulator of growth factor-induced Src mitogenic signaling [].This entry represents the N-terminal VHS (Vps27p/Hrs/Stam) domain of TOM1L2, which is found next to the GAT domain. The VHS domain has a superhelical structure similar to the structure of the ARM repeats [
].
TOM1-like protein 1 (TOM1L1) is an adapter protein involved in signaling pathways. It interacts with the SH2 and SH3 domains of various signaling proteins when it is phosphorylated. TOM1L1 promotes activation of Src family tyrosine kinase Fyn, possibly by disrupting intramolecular SH3-dependent interactions [
]. It has been implicated in multivesicular body (MVB) formation, viral egress from the cell, and cytokinesis. Its amplification enhances the metastatic progression of ERBB2-positive breast cancers [,
,
].This entry represents the N-terminal VHS (Vps27p/Hrs/Stam) domain of TOM1L1, which is found next to the GAT domain (
). This domain has a superhelical structure similar to the structure of the ARM repeats [
].
This is C-terminal domain of Nup188. It is a right-handed arc-shaped superhelical structure built from 19 helices that form 6 helical repeats, which are stacked in regular order. The first helical pair (alpha1 and alpha2) forms a HEAT repeat followed by 5 ARM repeats [
].
Virtually all mitochondrial precursors are imported via the same mechanism [
]: precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, 4 of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the 2 subcomplexes possibly binding via their trans-membrane (TM) regions -the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 []. The human homologue of the fungal MAS20 (TOM20) import receptor has been identified and characterised [
]. Although the amino acid sequences exhibit pronounced differences, similarity is greatest in the N-terminal third of the molecules. The structure of the rat TOM20 import receptor has been determined by NMR []. The cytosolic domain forms an all-alpha structure, with a hydrophobic groove that mediates presequence binding [].
This entry contains Influenza virus matrix protein 2. It is an integral membrane protein that is expressed on the infected cell surface and incorporated into virions where it is a minor component. The protein spans the viral membrane with an extracellular amino-terminus and a cytoplasmic carboxy-terminus. The transmembrane domain of the M2 protein forms the channel pore. The M2 protein, which forms a homotetramer, has H ion channel which was found to be regulated by pH [] and may have a pivotal role in the biology of Influenza virus infection [].
The Gp7 protein contains a DNA-binding function and may have a role in mediating the structural transition from prohead to mature virus and also scaffold release [
]. Gp7 is arranged within the capsid as a series of concentric shells [].The structure of Gp7 forms a dimer that resemble arrows, with a four-helix bundle composing the arrowhead and a coiled coil forming the tail [
].
This entry describes the Carboxysome shell vertex protein CsoS4A (also known as carboxysome operon protein orfA). It distinguishes one of the two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins are components of other shells, for example, the ethanolamine utilization protein EutN/carboxysome structural protein Ccml of the ethanolamine degradation organelle of Nitrobacter hamburgensis. This protein, together with CsoS4B, forms vertices in the carboxysome [
].
This entry describes the Carboxysome shell vertex protein CsoS4B (also known as carboxysome operon protein orfB). It distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins are components of other types of shell such as the shell of the ethanolamine degradation organelle. This protein, together with CsoS4A, forms vertices in the carboxysome [
].
Uncharacterised conserved protein UCP029389, subtilisin-related
Type:
Family
Description:
This entry contains proteins related to subtilisin-type serine proteases that belong to MEROPS peptidase family S8 but are classed as non-peptidase homologues, and which have no known function.
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length.
Foamy virus (FV) gene expression is strictly dependent on their transactivator proteins called Bel1/Tas. The presence of a functionally active, internal promoter, besides the conventional LTR promoters, is unique to FVs. The nuclear Bel1/Tas protein of primate prototype FV binds DNA target sites directly and consists of at least two functional domains, an N-terminal/central DNA binding and a C-terminal activation domain [
].
Transport ATPases can be lumped into four distinct types, P, F, V, and ABC. The transport ATPase field is paving the way for nanotechnology focused on nano-motors using the F-type ATPases (F(0)F(1)). When these ATPases are driven in reverse by a proton gradient, they have the capacity to interconvert electrochemical energy into mechanical energy and finally into chemical energy, which is conserved in the terminal bond of ATP [
]. This group represents a F-type ATP synthase, subunit I.
Uncharacterised conserved protein UCP031890, Tim44-related
Type:
Family
Description:
This group consists of bacterial uncharacterised proteins containing a Tim44-like domain (
). Their function is unknown, but a role in transport seems likely.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they may be membrane-anchored (based on transmembrane segment prediction).
Uncharacterised conserved protein UCP032162, transmembrane
Type:
Family
Description:
There is currently no experimental data for members of this group of proteins or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins.
This entry includes Bacteriophage D3, Orf41.6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.The members of this family are all sequences found within hypothetical proteins expressed by various bacteria, archaea and phage. The region concerned is approximately 150 residues long.
Members of this family are the accessory protein XdhC, found in bacteria, that is responsible for insertion of the molybdenum cofactor into the xanthine dehydrogenase large chain, XdhB. This protein is not part of the mature xanthine dehydrogenase. Xanthine dehydrogenase is an enzyme for purine catabolism, from other purines to xanthine to urate to further breakdown products.
Bacillus/Clostridium Ger spore germination protein
Type:
Family
Description:
Dormant Bacillus subtilis spores germinate in the presence of particular nutrients called germinants. The spores are thought to
recognise germinants through receptor proteins encoded by the gerA family of operons, which includes gerA, gerB, and gerK []. The GerA proteins are predicted to be membrane associated.
Bacterial microcompartments (BMCs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. They are found across bacteria where they play functionally diverse roles including CO(2) fixation and the catabolism of a range of organic compounds. They function as organelles by sequestering particular metabolic processes within the cell. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products (including toxic or volatile intermediates) into and out of the lumen. Although functionally distinct BMCs vary in their encapsulated enzymes, all are defined by homologous shell proteins. The shells of BMCs are made primarily of a family of proteins whose structural core is the BMC domain, and variations upon this core provide functional diversity [
,
,
]. This entry represents carboxysome shell protein CcmL and similar proteins from cyanobacteria. CcmL, which adopts a pentameric assembly, forms vertices in the carboxysome, a polyhedral BMC where RuBisCO (ribulose bisphosphate carboxylase) is sequestered. It induces curvature upon insertion into an otherwise flat hexagonal molecular layer of CcmK subunits (
) [
,
].
The family includes the triplex capsid protein 1 (TRX1, UL38 or VP19C) from herpesviruses, which is a structural component of the icosahedral capsid. The capsid is composed of pentamers and hexamers of the major capsid protein, which are linked together by heterotrimers called triplexes. These triplexes are formed by a single molecule of TRX1 and two copies of triplex protein 2 (TRX2) [
,
,
]. Additionally, TRX1 is required for efficient transport of TRX2 to the nucleus, which is the site of capsid assembly [].
The LiaRS two-component system is part of the regulatory network orchestrating the cell-envelope stress response in Bacillus subtilis. It responds to perturbations with the cell envelope, especially antibiotics that interfere with the lipid II and undecaprenol cycle, such as bacitracin or vancomycin. LiaRS-dependent regulation is strictly repressed by the membrane protein LiaF and it integrates both positive and negative feedback loops to transduce cell envelope stress signals [
,
]. This entry represents a group of cell wall-active antibiotic response proteins, including LiaF and YvqF types.
RPL14 is a component of the large ribosomal subunit in both archaea and eukaryotes with KOW motif at its N terminus [
]. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4 []. Although RPL14 is well conserved, it is not found in all archaea, and therefore it is presumably not essential [].
RPL26 and its bacterial paralogue RPL24 have a KOW motif at their N-terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4 [
]. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits []. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly []. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage [].
RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. The KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4 []. RPS4 deficiency in human has been associated with Turner syndrome. Archaeal RPS4 (RPS4e) showed substantial identity to the eukaryotic equivalents RPS4, but the archaeal proteins formed a different complex from the eukaryotic proteins [].
This entry represents coenzyme PQQ biosynthesis protein E, which is a prototypical peptide-cyclising radical SAM enzyme. It links a Tyr to a Glu as the first step in the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ) from the precursor peptide PqqA. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.This entry also includes some other radical SAM enzymes, such as tungsten-containing aldehyde ferredoxin oxidoreductase cofactor-modifying protein, adoMet-dependent heme synthase [
] and Fe-coproporphyrin III synthase [].
This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis [
,
]. PqqD functions as a PqqA binding protein that would serve as a chaperone to deliver PqqA to PqqE [].
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity []:Serine/threonine-protein kinasesTyrosine-protein kinasesDual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins)Protein kinase function is evolutionarily conserved from Escherichia coli to human [
]. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases [].This group represents a protein kinase C, alpha/beta/gamma types.
This entry represents the novel protein kinase C (nPKC) family.The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [
,
,
].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [
,
]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [,
,
]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.
