RelA/SpoT family protein is involved in guanosine tetraphosphate metabolic process, such as GTP pyrophosphokinase that catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp; contains HD, nucleotidyltransferase (NT), TGS, alpha helical (AH), Ribosome-InterSubunit (RIS) and ACT domains
(p)ppGpp synthetase, RelA/SpoT family; The functions of E. coli RelA and SpoT differ somewhat. ...
58-716
0e+00
(p)ppGpp synthetase, RelA/SpoT family; The functions of E. coli RelA and SpoT differ somewhat. RelA (EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. [Cellular processes, Adaptations to atypical conditions]
Pssm-ID: 213552 [Multi-domain] Cd Length: 683 Bit Score: 595.52 E-value: 0e+00
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
241-350
2.15e-58
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologs in plants and in other eubacteria. RelA is a guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5) while SpoT is thought to be a bifunctional enzyme catalysing both ppGpp synthesis and degradation (ppGpp 3'-pyrophosphohydrolase, (EC:3.1.7.2)). This region is often found in association with HD (pfam01966), a metal-dependent phosphohydrolase, TGS (pfam02824) which is a possible nucleotide-binding region, and the ACT regulatory domain (pfam01842).
Pssm-ID: 428031 [Multi-domain] Cd Length: 113 Bit Score: 192.76 E-value: 2.15e-58
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
241-350
1.42e-55
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ somewhat. RelA produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Pssm-ID: 214934 [Multi-domain] Cd Length: 111 Bit Score: 185.08 E-value: 1.42e-55
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
220-339
4.05e-35
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition.Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism.
Pssm-ID: 143389 [Multi-domain] Cd Length: 129 Bit Score: 129.39 E-value: 4.05e-35
(p)ppGpp synthetase, RelA/SpoT family; The functions of E. coli RelA and SpoT differ somewhat. ...
58-716
0e+00
(p)ppGpp synthetase, RelA/SpoT family; The functions of E. coli RelA and SpoT differ somewhat. RelA (EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. [Cellular processes, Adaptations to atypical conditions]
Pssm-ID: 213552 [Multi-domain] Cd Length: 683 Bit Score: 595.52 E-value: 0e+00
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
241-350
2.15e-58
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologs in plants and in other eubacteria. RelA is a guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5) while SpoT is thought to be a bifunctional enzyme catalysing both ppGpp synthesis and degradation (ppGpp 3'-pyrophosphohydrolase, (EC:3.1.7.2)). This region is often found in association with HD (pfam01966), a metal-dependent phosphohydrolase, TGS (pfam02824) which is a possible nucleotide-binding region, and the ACT regulatory domain (pfam01842).
Pssm-ID: 428031 [Multi-domain] Cd Length: 113 Bit Score: 192.76 E-value: 2.15e-58
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
241-350
1.42e-55
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ somewhat. RelA produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Pssm-ID: 214934 [Multi-domain] Cd Length: 111 Bit Score: 185.08 E-value: 1.42e-55
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
220-339
4.05e-35
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition.Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism.
Pssm-ID: 143389 [Multi-domain] Cd Length: 129 Bit Score: 129.39 E-value: 4.05e-35
TGS (ThrRS, GTPase and SpoT) domain found in the RelA/SpoT homolog (RSH) family; The RelA/SpoT ...
396-454
2.24e-33
TGS (ThrRS, GTPase and SpoT) domain found in the RelA/SpoT homolog (RSH) family; The RelA/SpoT homolog (RSH) family consists of long RSH proteins and short RSH proteins. Long RSH proteins have been characterized as containing an N-terminal region and a C-terminal region. The N-terminal region contains a pseudo-hydrolase (inactive-hydrolase) domain and a (p)ppGpp synthetase domain. The C-terminal region contains a ubiquitin-like TGS (ThrRS, GTPase and SpoT) domain, a conserved cysteine domain (CC), helical and ACT (aspartate kinase, chorismate mutase, TyrA domain) domains connected by a linker region. Short RSH proteins have a truncated C-terminal region without ACT domain. The RSH family includes two classes of enzyme: i) monofunctional (p)ppGpp synthetase I, RelA, and ii) bifunctional (p)ppGpp synthetase II/hydrolase, SpoT (also called Rel). Both classes are capable of synthesizing (p)ppGpp but only bifunctional enzymes are capable of (p)ppGpp hydrolysis. SpoT is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. The function of the TGS domain of SpoT is in transcription of survival and virulence genes in respond to environmental stress. RelA is an ATP:GTP(GDP) pyrophosphate transferase that is recruited to stalled ribosomes and activated to synthesize (p)ppGpp, which acts as a pleiotropic secondary messenger.
Pssm-ID: 340459 [Multi-domain] Cd Length: 59 Bit Score: 121.86 E-value: 2.24e-33
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
395-454
1.00e-21
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organizm, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Pssm-ID: 427005 [Multi-domain] Cd Length: 60 Bit Score: 88.76 E-value: 1.00e-21
ACT domain found C-terminal of the RelA/SpoT domains; ACT_RelA-SpoT: the ACT domain found ...
645-716
2.69e-19
ACT domain found C-terminal of the RelA/SpoT domains; ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes in E. coli, a bifunctional Rel/Spo protein has been discovered in most gram-positive organisms studied so far. These bifunctional Rel/Spo homologs (rsh) appear to modulate (p)ppGpp levels through two distinct active sites that are controlled by a reciprocal regulatory mechanism ensuring inverse coupling of opposing activities. In studies with the Streptococcus equisimilis Rel/Spo homolog, the C-terminal domain appears to be involved in this reciprocal regulation of the two opposing catalytic activities present in the N-terminal domain, ensuring that both synthesis and degradation activities are not coinduced. Members of this CD belong to the superfamily of ACT regulatory domains.
Pssm-ID: 153148 [Multi-domain] Cd Length: 71 Bit Score: 82.50 E-value: 2.69e-19
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
397-453
3.43e-11
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; This family includes eukaryotic and some bacterial threonyl-tRNA synthetases (ThrRSs), a distinct Obg family GTPases, and guanosine polyphosphate hydrolase (SpoT) and synthetase (RelA), which are involved in stringent response in bacteria, as well as uridine kinase (UDK) from Thermotogales. All family members contain a TGS domain named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. It is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. The functions of the TGS domain remains unclear, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, with a regulatory role.
Pssm-ID: 340455 [Multi-domain] Cd Length: 61 Bit Score: 59.16 E-value: 3.43e-11
ACT domains are commonly involved in specifically binding an amino acid or other small ligand ...
645-706
1.13e-06
ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times.
Pssm-ID: 153139 [Multi-domain] Cd Length: 60 Bit Score: 46.13 E-value: 1.13e-06
ACT domain; This family of domains generally have a regulatory role. ACT domains are linked to ...
644-710
1.45e-06
ACT domain; This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95, which is inhibited by serine. Aspartokinase EC:2.7.2.4, which is regulated by lysine. Acetolactate synthase small regulatory subunit, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51. formyltetrahydrofolate deformylase EC:3.5.1.10, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5
Pssm-ID: 426468 [Multi-domain] Cd Length: 66 Bit Score: 46.15 E-value: 1.45e-06
TGS (ThrRS, GTPase and SpoT) domain found in Methanocaldococcus jannaschii uncharacterized ...
403-454
1.32e-04
TGS (ThrRS, GTPase and SpoT) domain found in Methanocaldococcus jannaschii uncharacterized GTP-binding protein MJ1332 and similar proteins; This family includes a group of uncharacterized GTP-binding proteins from archaea, which belong to the Obg family of GTPases. The family members contain a domain of characteristic Obg-type G-motifs that may be the core of GTPase activity, as well as a C-terminal TGS (ThrRS, GTPase and SpoT) domain that has a predominantly beta-grasp ubiquitin-like fold.
Pssm-ID: 340460 [Multi-domain] Cd Length: 78 Bit Score: 40.76 E-value: 1.32e-04
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
400-458
1.82e-04
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases
Pssm-ID: 440210 [Multi-domain] Cd Length: 639 Bit Score: 44.64 E-value: 1.82e-04
ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate ...
650-715
3.09e-04
ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. This CD also includes the C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillus, and Treponema species. LSD enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in E. coli, and other Enterobacteriales, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Pssm-ID: 153151 Cd Length: 71 Bit Score: 39.76 E-value: 3.09e-04
C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; ...
644-714
3.95e-04
C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Pssm-ID: 153175 Cd Length: 71 Bit Score: 39.44 E-value: 3.95e-04
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, ...
647-693
5.69e-03
ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR interacts directly with GcvA rather than binding to DNA to cause repression. Members of this CD belong to the superfamily of ACT regulatory domains.
Pssm-ID: 153141 [Multi-domain] Cd Length: 81 Bit Score: 36.43 E-value: 5.69e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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