This entry represent a group of insect proteins, including protamine A (ProtA), protamine B (ProtB) and protamine-like protein 99C (Prtl99C) from Drosophila melanogaster. They contain a HMG-box and are involved in chromatin compaction during spermiogenesis [
,
]. Prtl99C is a sperm chromatin-associated protein that is essential for male fertility [].
M-phase inducer phosphatases function as dosage-dependent inducers in mitotic control [
,
,
,
]. They are tyrosine protein phosphatases required for progression of the cell cycle. They may directly dephosphorylate p34(cdc2) and activate p34(cdc2) kinase activity. They catalyse the reaction:protein tyrosine phosphate + H2O = protein tyrosine + P
i
This entry represents a family of proteins from bacteria and some fungal species, including YBR137W from Saccharomyces cerevisiae (
). This protein may play a role in the regulation of tail-anchored (TA) protein targeting. It shows an antiparallel β-sheet made of four β-strands surrounded by seven α-helices [
,
].
This entry represents Aftiphilin and related proteins from animals, including Uncharacterised protein CLBA1 (Clathrin-binding box of aftiphilin-containing protein 1). Aftin forms a stable complex with p200 and gamma-synergin [
]. It may play a role in membrane trafficking. Aftiphilin contains a clathrin box, with two identified clathrin-binding motifs [,
].
Protein import into the mitochondria involves several translocase complexes: the preprotein translocase of the outer mitochondrial membrane (TOM complex) and the two preprotein translocases of the inner mitochondrial membrane (called TIM complexes).This entry represents TOM6 from the plant TOM complex, which consist at least of six subunits [
,
].
This entry describes an uncharacterised small, hydrophobic protein of about 50 amino acids, known as XapX found between the xapB and xapR genes of the Escherichia coli xanthosine utilization system. It is also found in a number of other small proteins, such as the N-terminal region of proteins modeled by
.
This is a family of small (less than 200 residue long) proteins that are conserved from fungi to humans. Family members include the TVP18 Golgi membrane proteins that are involved in vesicular trafficking [
] and the calcium channel flower proteins, which form calcium channels that regulate synaptic endocytosis [].
Each chondroitin proteoglycan (CPG) consists of a protein core and one or more covalently attached chondroitin chains. Nine chondroitin core proteins have been identified in C. elegans (CPG-1 to CPG-9) [
]. This family includes proteins known as chondroitin proteoglycan 3 (CPG-3) and is found in nematodes from the class Chromadorea.
Members of this protein family are found exclusively in genomes that contain putative set of labile selenium-dependent enzyme accessory proteins as well as homologues of a labile selenium-dependent purine hydroxylase. A mutant in this gene in Escherichia coli had improved stationary phase viability. The function of this protein is unknown.
This domain present in an uncharacterized family of proteins found in bacteria and archaea. These proteins also have a C-terminal CCC1-like transmembrane domain and are thought to be involved in iron and/or manganese transport. This domain has the conserved residues of a di-iron centre found in other ferritin-like proteins [
].
This is a family of spirochete major outer sheath protein C-terminal regions. These proteins are present on the bacterial cell surface. In Treponema denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [
].
This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In Treponema denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [
].
Pal1 is a membrane associated protein that is involved in the maintenance of cylindrical cellular morphology. It localises to sites of active growth. Pal1 physically interacts and displays overlapping localisation with the Huntingtin-interacting-protein (Hip1)-related protein Sla2p/End4p [
]. Fission yeast Pal1 is involved in cellular morphogenesis and cell wall integrity [].
Short myomegalin-like EB1 binding protein, N-terminal
Type:
Domain
Description:
This N-terminal region is found in SMYLE (for short myomegalin-like EB1 binding protein). It includes the SMYLE homology (SmyH) domain found in the first 100 residues at the N terminus. This conserved SmyH domain is required and sufficient for PKA scaffolding protein AKAP9, and the pericentrosomal protein CDK5RAP2 binding [
].
This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [
,
]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.
This entry represents Glutaredoxin-1 (GLRX1) and similar proteins predominantly found in animals and poxvirus. The animal members of this protein family have glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. They reduce low molecular weight disulfides and proteins. Viral members have thioltransferase and dehydroascorbate reductase activities [
].
This family consists mainly of Neisseria meningitidis TspB virulence factor proteins. Proteins in this family also include attachment protein G3P from Pseudomonas phage Pf3. G3P plays essential roles both in the penetration of the viral genome into the bacterial host via pilus retraction and in the extrusion process [
].
This family of proteins is largely uncharacterised. They were annotated as ribosomal SSU S4 p proteins but there is not evidence supporting this, and it is, apparently, a missannotation. Sequences in this entry are found in gammaproteobacteria. Proteins in this family are typically between 162 to 178 amino acids in length.
This domain is functionally uncharacterised, and it is found in eukaryotic proteins such as TBC1 domain family member 1 and 4 (TBC1D1 and TBCD4). This presumed domain is typically between 50 to 64 amino acids in length. TBC1 and 4 may act as GTPase-activating proteins for Rab family proteins [
].
This is the BAR (Bin/amphiphysin/Rvs) domain of Sortin nexin 8 (Snx8), which can sense, stabilise and induce membrane curvature [
]. These proteins are involved in intracellular protein transport from early endosomes to the trans-Golgi network []. Its yeast counterpart, Mvp1 is required for sorting proteins to the vacuole [].
This entry represents a group of periplasmic solute-binding proteins that are part of tripartite ATP-independent periplasmic (TRAP) transport systems, including the periplasmic protein TakP, which is involved in the uptake of alpha-keto acids [
]; periplasmic protein All3028, which specifically binds monocarboxylate 2-oxoacids []; and TTHA0766, which binds binds L-lactate [].
This entry represents an Ig domain found in the uncharacterized human protein C19orf38, which is found across mammals. Family members have one predicted transmembrane region which is not included in this entry. The C19orf38 protein is also known as HIDE1 after Highly expressed in Immature DEndritic cell transcript 1 protein.
This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 79 and 98 amino acids in length. The region contains two predicted transmembrane helices. The eukaryotic examples are found in the Foraminiferan Reticulomyxa filosa that contains several proteins with this family.
The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three α-helices [
].
This group represents the neuroblastoma suppressor of tumorigenicity 1 protein, also known as zinc finger protein DAN. This protein is a possible candidate for a tumor suppressor of neuroblastoma and may play an important role in preventing cells from entering the final stage (G1/S) of the transformation process [
].
This entry represents a group of plant FCS-Like Zinc finger proteins, including FLZ12/13/14 from Arabidopsis [
]. They are adaptor proteins which facilitate the interaction of kinase SnRK1 with other proteins []. The FLZ domain of FLZ12 alone has been found to be sufficient to mediate interaction with SnRK1alpha subunit [].
This entry represents a domain found at the N-terminal end of eukaryotic proteins, including Protein LLP from Aplysia kurodai, a transcriptional activator required for long-term synaptic facilitation at the sensory motor synapse [
], and several proteins that belong to the UPF0642 family. The function of this domain is not known.
Clitocypin binds and inhibits cysteine proteinases. It has no similarity to any other known cysteine proteinase inhibitors but bears some similarity to a lectin-like family of proteins from mushrooms [
]. Insecticidal potential of clytocypins has been studied on colorado potato beetle, and thus, these are promising candidates for biopesticides [].
The UL46 protein (VP11/12) is
produced in the late phase of Herpes virus infection in a manner highly dependent on viral DNA synthesis, and is mainly distributed at the edge of the nucleus in the cytoplasm. It is a tegument phosphoprotein reported to modulate the activity of UL48 (anti-TNF) protein.
This is a family of bacterial proteasome cofactors. The family member from Mycobacterium tuberculosis, protein Rv3780, was shown to form rings and cap proteasome core particles. It enhanced peptide and protein degradation by proteasomes in an adenosine triphosphate (ATP)-independent manner, promoting degradation of the heat shock protein repressor HspR [
].
The function of this family of transmembrane proteins is unknown. In vertebrates, proteins in this family are located in the lysosomal membrane and late endosome [
,
]. In Arabidopsis, a member of this family (protein FIP1) has been found to weakly interact with FRIGIDA, a determinant of flowering time [].
Potassium channels are the most diverse group of the ion channel family [
,
]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group.These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K
+channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes [
]. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis [].All K
+channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K
+selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K
+across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K
+channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K
+channels; and three types of calcium (Ca)-activated K
+channels (BK, IK and SK) [
]. The 2TM domain family comprises inward-rectifying K+channels. In addition, there are K
+channel alpha-subunits that possess two P-domains. These are usually highly regulated K
+selective leak channels.
2P-domain channels influence the resting membrane potential and as a result can control cell excitability. In addition, they pass K+
in response to changes in membrane potential, and are also tightly regulated by molecular oxygen, GABA (gamma-aminobutyric acid), noradrenaline and serotonin.The first member of this family (TOK1), cloned from Saccharomyces cerevisiae [
], ispredicted to have eight potential transmembrane (TM) helices. However,
subsequently-cloned two P-domain family members from Drosophila andmammalian species are predicted to have only four TM segments. They are
usually referred to as TWIK-related channels (Tandem of P-domains in a Weakly Inward rectifying K+ channel) [
,
,
,
]. Functional characterisation of these channels has revealed a diversity of properties in that they may show inward or outward rectification, their activity may be modulated in different directions by protein phosphorylation, and their sensitivity to changes in intracellular or extracellular pH varies. Despite these disparate properties, they are all thought to share the same topology offour TM segments, including two P-domains. That TWIK-related K+ channels
all produce instantaneous and non-inactivating K+ currents, which do notdisplay a voltage-dependent activation threshold, suggests that they are
background (leak) K+ channels involved in the generation and modulation of the resting membrane potential in various cell types. Further studies have revealed that they may be found in many species, including: plants, invertebrates and mammals.TWIK family members (TWIK-1 and TWIK-2) produce constitutive K+ currents of weak amplitude [
]. They are present in a variety of tissues, including brain and cells of the immune system. Together with their functional properties, their wide distribution suggests that these channels may be involved in the control of background K+ conductances in many cell types.TWIK-1 was the first two P-domain K
+channel subunit cloned from human
tissue []. It is widely distributed, being particularly abundant in thebrain and heart. It forms a weak inward rectifer K
+channel, and has been
found to be inhibited by internal acidification; its activity is enhancedby protein kinase C phosphorylation.
This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [
], and both of these regions are represented in this family.
The Sgf11 (SAGA-associated factor 11) family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [
].
Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8)
. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.
This entry represents a leucine rich repeat. A leucine-rich repeat (LRR) is a protein structural motif that forms an alpha/beta horseshoe fold [
,
]. Leucine-rich repeats are frequently involved in the formation of protein protein interactions [,
].This repeat is found in a large number of BSPA-like surface antigens from Trichomonas vaginalis.
Proteins containing this domain include lysophosphatidylcholine acyltransferase 1 (LPCAT1) and related proteins. LPCAT1 exhibits acyltransferase activity [
], [] and is involved in LD (lipid droplet)-associated lipid metabolism [,
]. Proteins containing this domain also includes glycerol-3-phosphate acyltransferases, such as GPAT3 and GPAT4, which are involved in de novo triacylglycerol synthesis [,
].
This superfamily represents a domain found at the N terminus of nuclear valosin-containing protein (VCP)-like protein 2 (NVL2). This domain adopts a three helix fold resembling part of a winged helix motif and binds to nucleolin, a multifunctional phosphoprotein ubiquitously distributed in the nucleolus, nucleus and cytoplasm of the cell [
].
YfgM is a subunit of the ancillary SecYEG translocon that may mediate protein transfer from the SecYEG translocon to the periplasmic chaperone network via its periplasmic C-terminal region [
]. It may coordinate stress responses across the inner membrane via a dynamic protein-protein interaction network inside and outside of the membrane [].
This entry represents the N-terminal domain found in the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica []. Proteins containing this domain belong to the molybdopterin_binding superfamily of proteins.
This entry represents the ZZ type zinc finger found in HERC2 and related proteins. HERC2 is an E3 ubiquitin-protein ligase that regulates ubiquitin-dependent retention of repair proteins on damaged chromosomes [
]. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding [,
,
].
This family includes DNA-binding protein MJ1563, putative HTH-type transcriptional regulator yvbF, uncharacterised protein yuaC, and putative HTH-type transcriptional regulator yvaV. All family members are predicted to have a helix-turn-helix (HTH) motif, which is a major structural motif capable of binding DNA. Many proteins with this motif have been shown to regulate gene expression.
Kappa-casein is a mammalian milk protein involved in a
number of important physiological processes []. In the gut,the ingested protein is split into an insoluble peptide
(para kappa-casein) and a soluble hydrophilic glycopeptide(caseinomacropeptide). Caseinomacropeptide is responsible
for increased efficiency of digestion, prevention of neonatehypersensitivity to ingested proteins, and inhibition of
gastric pathogens.
This EGF-like domain is found at the C terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite [].
This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [
].
This family consists of several Orthopoxvirus A26L and A30L proteins. The Vaccinia A30L gene is regulated by a late promoter and encodes a protein of approximately 9kDa. It is thought that the A30L protein is needed for vaccinia virus morphogenesis, specifically the association of the dense viroplasm with viral membranes [
].
This family consists of several plant specific Systemin and Prosystemin proteins. Systemin is processed from a larger prohormone protein, called prosystemin, by proteolytic cleavages [
]. Systemin activates a lipid-based signal transduction pathway in which linolenic acid is converted to jasmonic acid, a potent activator of defense gene transcription, including proteinase inhibitor [].
This family consists of several Pneumovirus M2-2 proteins. The M2-2 protein acts as a regulatory factor that mediates the switch from transcription to RNA replication [
]. It acts late in infection in which it inhibits viral transcription and up-regulates RNA replication [,
], mediated by phosphorylation of the P protein [].
Members of this protein family are PimC proteins that can be found in Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Pimeloyl-CoA, is a catabolite of benzoyl-CoA degradation, which occurs in R. palustris. This entry represents the large subunit.
Members of this protein family are PimD proteins, and can be found in Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Pimeloyl-CoA is a catabolite of benzoyl-CoA degradation, which occurs in R. palustris. This entry represents the small subunit
Putative energy coupling factor transporter S component
Type:
Family
Description:
This family of proteins is restricted to the Mollicutes. Members belong to a superfamily of multiple membrane-spanning proteins, among which those with assigned activities function as the S component (the specificity component) of ECF transporters. However, members of this family are not recognised by other entries for S component proteins (
).
This domain has a ubiquitin-like fold found in a diverse range of proteins including RNP25 [
]. RNP25 is a component of the U11/U12 snRNPs that are part of the U12-type spliceosome. It contains a conserved ubiquitin-like (Ubl) domain with a β-grasp Ubl fold, a common structure involved in protein-protein interactions [,
].
Members of this family are putative addiction module antidote proteins encoded by genes that appear recurrently in two-gene operons, where the other gene encodes a Doc (death-on-curing) protein (
). Many family members contain an AbrB-like domain (
). Note that these proteins tend to be found on bacterial chromosomes, not on plasmids.
This entry represents a bacterial family of proteins that includes several putative HNH endonucleases that form part of antiviral defense systems such as Ec78, Ec83 and Vc95. These proteins confer protection against specific phages [
].This entry also includes Septu protein PtuB, a component of antiviral defense system Septu type II [
].
Putative conjugal transfer nickase/helicase TraI, C-terminal
Type:
Domain
Description:
This entry contains proteins some of which are from pathogenic strains of Gammaproteobacteria. Though the function of these proteins is unknown, they could be involved in pathogenesis. This domain is found at the C terminus of proteins that contain a N-terminal metal-dependent phosphohydrolase (HD) region and are considered to be helicases/relaxases [
].
Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the C-terminal domain whose function is unclear. It is found C-terminal to the Hsp90 chaperone (heat shock protein 90) binding domain (
) and the N-terminal kinase binding domain of Cdc37 (
) [
].
This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the Saccharomyces cerevisiae Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants [].
This family includes nuclear envelope protein YPR174C and NAP1-binding protein (NBP1). Both proteins bind to the nuclear membrane. NBP1 has been shown in Saccharomyces cerevisiae to function in spindle pole body duplication [
] and YPR174C may be involved in the connection of the spindle pole body to the nuclear envelope [].
Tetrahydromethanopterin S-methyltransferase subunit B
Type:
Family
Description:
Members of this protein family are the MtrB protein of the tetrahydromethanopterin S-methyltransferase complex. This system is universal in archaeal methanogens [
]. The N5-methyltetrahydromethanopterin: coenzyme M (
) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump [
].
The matrix proteins of Pneumovirus are transcriptional processivity and antitermination factor, and play a crucial role in viral assembly.This superfamily represents the N-terminal domain found in Pneumovirus matrix protein. Structurally, it consists of 8 beta strands and 3 alpha helices. Within Pneumovirus matrix protein, this domain is believed to mediate species-specific interactions.
This C2H2 type zinc-finger is found at the N terminus of SCNM1, sodium channel modifier protein 1 [
]. Phylogenetic analysis of these zinc finger sequences places SCNM1 within the U1C subfamily of RNA binding proteins that is commonly found in RNA-processing proteins, suggesting that SCNM1 is involved in splicing activities [].
This entry represents proteins predicted to function as serpins from various poxviruses, such as protein K3 from Vaccinia virus. Serpins are serine protease inhibitors. Protein K3 plays an integral role in the resistance of the virus to interferon and may bind competitively to P1 kinase in order to block eIF-2-alpha phosphorylation [
].
This entry represents a domain found at the N terminus of nuclear valosin-containing protein (VCP)-like protein 2 (NVL2). This domain adopts a three helix fold resembling part of a winged helix motif and binds to nucleolin, a multifunctional phosphoprotein ubiquitously distributed in the nucleolus, nucleus and cytoplasm of the cell [
].
Bcl-2-modifying factor (BMF) is thought to play a role in inducing apoptosis. It is thought to bind to Bcl-2 proteins [
]. This family of proteins is found in eukaryotes. Proteins in this family are typically between 75 and 190 amino acids in length. There are two conserved sequence motifs: GNA and DQF.
The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold [
]. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].
The ROQ domain, found in the protein Roquin (and in the C. elegans protein 'regulation of longevity by E3 ubiquitin-protein ligase') is composed of three subdomains, I, II and III. This entry represents the second domain, ROQ II. Structural analysis reveals similarity of domain II to the helix-turn-helix (HTH) fold [
].
This family includes the yeast nuclear export factor Sac3 [
], and mammalian GANP/MCM3-associated protein, which facilitates the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle []. It also includes yeast Thp3 (THO-related protein 3), which may have a role in transcription elongation [].
This entry represents a group of RING-H2 finger proteins mostly from plants, including RING1 (also known as ATL55, At5g10380) and related proteins from Arabidopsis. RING1 is an E3 ubiquitin-protein ligase that may be involved in positive regulation of programmed cell death (PCD) by facilitating degradation of negative regulators of PCD [
].
This family consists of several leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown [
]. It contains an M23 metalloendopeptidase fold, but was found to be catalytically inactive as a metalloendopeptidase [].
This entry represents the mitochondrial import inner membrane translocase subunit Tim16 (also known as Pam16). Tim16 is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) [
]. In Saccharomyces cerevisiae (Baker's yeast), Tim16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].
The proteins in this entry are functionally uncharacterised.The entry contains the Escherichia coli (strain K12) protein YjgA (
),
which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or
it is associated with a different oligomeric complex that comigrates with ribosomal particles [
].
Amino acid permeases are integral membrane proteins involved in the transport
of amino acids into the cell. A number of such proteins have been found to beevolutionary related [
,
,
].These proteins seem to contain up to 12 transmembrane segments. The best conserved region
in this family is located in the second transmembrane segment.
Amino acid permeases are integral membrane proteins involved in the transport
of amino acids into the cell. A number of such proteins have been found to beevolutionary related [
,
,
].These proteins seem to contain up to 12 transmembrane segments. The best conserved region
in this family is located in the second transmembrane segment.
This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase [
].
Protamine-P3 family consists of protamine 3 (PRM3) proteins. PRM3 proteins localize in the elongated spermatid cytoplasm (but not in mature sperm) and have been shown to affect sperm mobility [
,
]. Despite their name, protamine, PRM3 proteins might not share the same function such as replacing somatic histones during spermiogenesis with other protamines [].
This superfamily consists of several hypothetical proteins of unknown function which appear to be found mainly in Helicobacter pylori. The structure of HP0721 protein consists of a bundle of four α-helices connected by loops and stabilised by hydrophobic interactions. It has been suggested that this protein might represent a novel H. pylori [
].
This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis [
,
]. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Members of this family are Bacteroidetes lineage putative lipoproteins that always occur in pairs with a radical SAM enzyme,
, from a branch of the radical SAM superfamily in which many members perform peptide or protein modifications. In some members, the region distal to the Cys of the putative lipoprotein cleavage motif is duplicated.
Proteins in this entry are designated TraJ and are found in a proposed transfer region of a class of conjugative transposon found primarily in the Bacteroides lineage. They are related to conjugation system proteins in the Proteobacteria, including TrbL of Agrobacterium Ti plasmids and VirB6. This entry represents the C-terminal domain of these proteins.
This is a family of phage tail assembly chaperone proteins from Siphoviridae phages. TACs are required for the morphogenesis of all long-tailed phages. The proposed function for the TAC is to coat the tape-measure protein to prevent it from forming unproductive complexes or precipitating before the tail tube protein has been incorporated [
].
The FAM124 domain belongs to the Vicnial oxygen chelatase (VOC) superfamily of proteins and is comprised of two tandem α/β domains. Residue conservation suggests that it might be enzymatic. Certain FAM124 domains fused to the TRADD-N domain are predicted to have secondarily lost their enzymatic activity and might be involved in protein-protein interactions [
].
This entry represents a family of Gram-negative bacterial proteins involved in the Dot/Icm type IVb transport system, including IcmS from Legionella pneumophila. Members are small acidic cytoplasmic proteins required for Dot/Icm-dependent activities [
]. IcmS is part of a subcomplex which recruits effector proteins and delivers them to the core transmembrane subcomplex [,
].
This entry contains proteins from Fijiviruses including P7-1 protein from Southern rice black-streaked dwarf virus (SRBSDV) and the probable non-structural 41.0 kDa protein from Maize rough dwarf virus (MRDV). P7-1 induces the formation of virus-containing tubules in infected plant and insect vector cells allowing its efficient transmission especially in high temperatures [
,
].
This family of transmembrane proteins includes the lipase maturation factors LMF1 and LMF2. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states [
]. LMF1 acts as a specific chaperone for dimeric lipases, required both for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway [,
].
This family contains a number of zona-pellucida-binding proteins that seem to be restricted to mammals. These are sperm proteins that bind to the 90kDa family of zona pellucida glycoproteins in a calcium-dependent manner [
]. These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur [].
This entry represents a domain found in uncharacterised proteins predominantly found in bacteria that includes DUF2383 domain-containing protein from Pseudomonas aeruginosa (
). This protein shows a ferritin-like topology with a four-helix-bundle fold that lacks metal-ion-binding site typical of the ferritin family but has a potential metal-binding site [
]. Its function is still unknown.
This entry represents the N-terminal domain, N1, of the pIII protein of the CTXphi bacteriophage of Vibrio cholerae. CTXphi is a ssDNA Inovirus. pIII is a minor coat protein. This domain interacts directly with the C terminus of TolA, a periplasmic protein of Vibrio cholerae itself as part of the infection mechanism [
].
This entry contains a C-terminal presumed zinc binding domain from the NINJA and related proteins, which interacts with the Tify domain of JAZ1 [
]. This domain appears to be necessary and sufficient for JAZ protein interaction. Proteins included in this entry play a role in stress-related and growth-related signalling cascades [,
,
].
This entry describes a region of approximately 16 residues found typically about 30 residues away from the C terminus of large numbers of proteins in the Planctomycetes, Lentisphaerae, and Verrucomicrobia, on proteins with a prepilin-type N-terminal cleavage/methylation domain (see
). The motif H-X(9)-D-G is nearly invariant. Single genomes may encode over 200 such proteins.
This entry describes a family of DNA-binding proteins widely conserved in Gram-positive bacteria, and occasionally occurring elsewhere, such as in Thermotoga [
,
].The family includes the sporulation regulator WhiA, which is required for expression of the ParB partioning protein during sporogenesis [
,
], as well as the uncharacterised protein MG103, found in mycoplasma.
This superfamily represents a β-barrel domain that is found in a family of bacterial proteins of unknown function. The crystal structure of such an uncharacterised protein (YP563039) from Shewanella denitrificans (strain OS217/ATCC BAA-1090/DSM 15013) at 1.80A resolution and of a protein with unknown function (SO1590) from Shewanella oneidensis MR-1 at 1.84A resolution have been solved.
This family consists of Salmonella SpvD (also known as VsdE) plasmid virulence proteins. The structure of the protein from Salmonella typhimurium has been solved and shows a papain-like fold, with a predicted catalytic triad of Cys73, His162 and Asp182. The protein has been shown to have deubiquitinating-like activity, releasing aminoluciferin (AML) from Ub-AML [
].
This family consists of several bacterial YopD like proteins. Virulent Yersinia species harbour a common plasmid that encodes essential virulence determinants (Yersinia outer proteins [Yops]), which are regulated by the extracellular stimuli Ca2+and temperature. YopD is thought to be a possible transmembrane protein and contains an amphipathic α-helix in its carboxy terminus [
].
Type VI secretion system peptidoglycan-associated domain
Type:
Domain
Description:
The flagellar motor protein MotB and the Gram-negative bacterial outer membrane protein OmpA (with an N-terminal outer membrane beta barrel domain) share a C-terminal peptidoglycan-associating homology region. This entry describes a domain found fused to type VI secretion system homologues of the type IV system protein DotU (see
), with OmpA/MotB homology [
].
This entry represents the N-terminal helix-turn-helix DNA-binding domain from the proteasome accessory factor C (PafC), which upregulates most of the genes induced by DNA damage. It mediates protein-DNA interactions as well as protein-protein interactions. The conformation of HTH exerts a regulatory mechanism, which prevents PafBC from efficient DNA binding under normal conditions [
].
Amino acid permeases are integral membrane proteins involved in the transport
of amino acids into the cell. A number of such proteins have been found to beevolutionary related [
,
,
].These proteins seem to contain up to 12 transmembrane segments. The best conserved region
in this family is located in the second transmembrane segment.
This superfamily represents an ~150-amino acid ADF-H (actin-depolymerising factor homology) domain found in three phylogenetically distinct classes of eukaryotic actin-binding proteins [
,
,
]. This domain shares structural similarity with another set of actin binding proteins, villin and gelsolin, and the C-terminal of the Sec23/Sec24 proteins. It consists of a mixed β-sheet structure.
This entry includes protein broad-minded, which interacts with cell cycle-related kinase (CCRK) and together these proteins regulate ciliary membrane and axonemal growth [
]; and phagosome assembly factor 1 (PHAF1) and its homologues. PHAF1 and BCAS3 form a complex that affects the recruitment of several core autophagy proteins to the phagophore assembly site [].
This entry represents the C terminus of the sperm centrosome protein speriolin [
,
].Speriolin is a sperm centrosome protein [
] that form a complex with CDC20, CDC27 and TUBG1. It interacts with Cdc20 and is only detected in testis in humans [,
]. The function of speriolin and speriolin-like proteins is unknown.
Arginine N-methyltransferase 2 is a delta-N-monomethylarginine transferase which monomethylates 'Arg-67' of ribosomal protein L12 [].Protein arginine methyltransferases (PRMT) have been implicated in the regulation of transcription. They are recruited to promoters via their interaction with transcription factors and exert their co-activator function by methylating arginine residues in histones and other chromatin proteins [
].
