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Conserved domains on  [gi|241913549|pdb|3HVZ|C]
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Chain C, Uncharacterized protein

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SpoT super family cl33835
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];
2-70 1.10e-38

(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];


The actual alignment was detected with superfamily member COG0317:

Pssm-ID: 440086 [Multi-domain]  Cd Length: 722  Bit Score: 134.90  E-value: 1.10e-38
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
3HVZ_C        2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTKE 70
Cdd:COG0317 391 DLFPDEVYVFTPKGDVIELPRGATPLDFAYAIHTEVGHRCVGAKVNGRLVPLSTPLKNGDTVEIITSKN 459
 
Name Accession Description Interval E-value
SpoT COG0317
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];
2-70 1.10e-38

(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];


Pssm-ID: 440086 [Multi-domain]  Cd Length: 722  Bit Score: 134.90  E-value: 1.10e-38
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
3HVZ_C        2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTKE 70
Cdd:COG0317 391 DLFPDEVYVFTPKGDVIELPRGATPLDFAYAIHTEVGHRCVGAKVNGRLVPLSTPLKNGDTVEIITSKN 459
TGS_RSH cd01668
TGS (ThrRS, GTPase and SpoT) domain found in the RelA/SpoT homolog (RSH) family; The RelA/SpoT ...
 9-67 1.61e-31

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: 104.14  E-value: 1.61e-31
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*....
3HVZ_C       9 FVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLT 67
Cdd:cd01668  1 FVFTPKGDVVSLPKGATPIDFAYAIHTDVGNKCVGAKVNGKIVPLDYVLKNGDVVEIIT 59
spoT_relA TIGR00691
(p)ppGpp synthetase, RelA/SpoT family; The functions of E. coli RelA and SpoT differ somewhat. ...
 2-69 1.88e-26

(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: 100.16  E-value: 1.88e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
3HVZ_C          2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTK 69
Cdd:TIGR00691 356 DLFNEEIYVFTPKGDVVELPSGSTPVDFAYAVHTDVGNKCTGAKVNGKIVPLDKELENGDVVEIITGK 423
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 6-70 8.77e-26

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 98.32  E-value: 8.77e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
3HVZ_C         6 EEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTKE 70
Cdd:PRK10872 404 DRVYVFTPKGDVVDLPAGSTPLDFAYHIHSDVGHRCIGAKIGGRIVPFTYQLQMGDQIEIITQKQ 468
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 8-67 5.85e-20

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: 74.89  E-value: 5.85e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
3HVZ_C         8 VFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLT 67
Cdd:pfam02824  1 IRVYTPDGKVPDLPRGATPEDFAYAIHTSLAKKFIYAKVNGQLVGLDHPLEDGDVVEIVT 60
 
Name Accession Description Interval E-value
SpoT COG0317
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];
2-70 1.10e-38

(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];


Pssm-ID: 440086 [Multi-domain]  Cd Length: 722  Bit Score: 134.90  E-value: 1.10e-38
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
3HVZ_C        2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTKE 70
Cdd:COG0317 391 DLFPDEVYVFTPKGDVIELPRGATPLDFAYAIHTEVGHRCVGAKVNGRLVPLSTPLKNGDTVEIITSKN 459
TGS_RSH cd01668
TGS (ThrRS, GTPase and SpoT) domain found in the RelA/SpoT homolog (RSH) family; The RelA/SpoT ...
 9-67 1.61e-31

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: 104.14  E-value: 1.61e-31
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*....
3HVZ_C       9 FVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLT 67
Cdd:cd01668  1 FVFTPKGDVVSLPKGATPIDFAYAIHTDVGNKCVGAKVNGKIVPLDYVLKNGDVVEIIT 59
spoT_relA TIGR00691
(p)ppGpp synthetase, RelA/SpoT family; The functions of E. coli RelA and SpoT differ somewhat. ...
 2-69 1.88e-26

(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: 100.16  E-value: 1.88e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
3HVZ_C          2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTK 69
Cdd:TIGR00691 356 DLFNEEIYVFTPKGDVVELPSGSTPVDFAYAVHTDVGNKCTGAKVNGKIVPLDKELENGDVVEIITGK 423
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 6-70 8.77e-26

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 98.32  E-value: 8.77e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
3HVZ_C         6 EEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTKE 70
Cdd:PRK10872 404 DRVYVFTPKGDVVDLPAGSTPLDFAYHIHSDVGHRCIGAKIGGRIVPFTYQLQMGDQIEIITQKQ 468
TGS pfam02824
TGS domain; The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain ...
 8-67 5.85e-20

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: 74.89  E-value: 5.85e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
3HVZ_C         8 VFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLT 67
Cdd:pfam02824  1 IRVYTPDGKVPDLPRGATPEDFAYAIHTSLAKKFIYAKVNGQLVGLDHPLEDGDVVEIVT 60
PRK11092 PRK11092
bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase;
2-69 2.09e-19

bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase;


Pssm-ID: 236843 [Multi-domain]  Cd Length: 702  Bit Score: 80.16  E-value: 2.09e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
3HVZ_C         2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTK 69
Cdd:PRK11092 382 DLFPDEIYVFTPEGRIVELPAGATPVDFAYAVHTDIGHACVGARVDRQPYPLSQPLTSGQTVEIITAP 449
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 10-66 5.88e-10

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: 49.91  E-value: 5.88e-10
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|
3HVZ_C      10 VFTPK---GDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVL 66
Cdd:cd01616  2 VFTVGktpGTVFVMNKGATAYSCAMHLHEDYCRKSILALVDGQLWDMYYPLTKGDEIKFL 61
PRK09602 PRK09602
translation-associated GTPase; Reviewed
 16-69 2.03e-07

translation-associated GTPase; Reviewed


Pssm-ID: 236584 [Multi-domain]  Cd Length: 396  Bit Score: 45.95  E-value: 2.03e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
3HVZ_C        16 DVISLPIGSTVIDFAYAIHSAVGNR*IGAkVDGR---IVPIDYKVKTGEIIDVLTTK 69
Cdd:PRK09602 341 DAFLLPKGSTARDLAYKIHTDIGEGFLYA-IDARtkrRIGEDYELKDGDVIKIVSTA 396
TGS_MJ1332_like cd01669
TGS (ThrRS, GTPase and SpoT) domain found in Methanocaldococcus jannaschii uncharacterized ...
 16-67 1.95e-06

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: 41.15  E-value: 1.95e-06
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*
3HVZ_C      16 DVISLPIGSTVIDFAYAIHSAVGNR*IGAkVDGR---IVPIDYKVKTGEIIDVLT 67
Cdd:cd01669 25 DAILLKRGSTPRDLAYKIHTDLGKGFLYA-IDARtkmRLGEDYELKHGDVVKIVS 78
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 13-69 1.15e-05

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: 41.17  E-value: 1.15e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
3HVZ_C       13 PKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTK 69
Cdd:COG0441   7 PDGSVREFEAGVTVLDVAKSISPGLAKAAVAAKVNGELVDLSTPIEEDAELEIVTFD 63
TGS_ThrRS cd01667
TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar ...
 13-72 6.69e-04

TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar proteins; ThrRS, also termed cytoplasmic threonine--tRNA ligase, is a class II aminoacyl-tRNA synthetase (aaRS) that plays an essential role in protein synthesis by catalyzing the aminoacylation of tRNA(Thr), generating aminoacyl-tRNA, and editing misacylation. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. TGS is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340458 [Multi-domain]  Cd Length: 65  Bit Score: 34.39  E-value: 6.69e-04
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|
3HVZ_C      13 PKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLTTKELE 72
Cdd:cd01667  6 PDGSVKEFPKGTTPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDAELEILTFDDPE 65
TGS_DRG cd01666
TGS (ThrRS, GTPase and SpoT) domain found in developmentally regulated GTP binding protein ...
 12-67 1.18e-03

TGS (ThrRS, GTPase and SpoT) domain found in developmentally regulated GTP binding protein (DRG) family; DRG-1 and DRG-2 comprise a highly conserved DRG subfamily of GTP-binding proteins found in archaea, plants, fungi and animals. The exact function of DRG proteins is unknown, although phylogenetic and biochemical fraction studies have linked them to translation, differentiation and growth. Their abnormal expressions may trigger cell transformation or cell cycle arrest. DRG-1 and DRG-2 bind to DFRP1 (DRG family regulatory protein 1) and DFRP2, respectively. Both DRG-1 and DRG-2 contain a domain of characteristic Obg-type G-motifs that may be the core of GTPase activity, as well as the C-terminal TGS (ThrRS, GTPase and SpoT) domain, which has a predominantly beta-grasp ubiquitin-like fold and may be related to RNA binding. DRG subfamily belongs to the Obg family of GTPases.


Pssm-ID: 340457 [Multi-domain]  Cd Length: 77  Bit Score: 33.75  E-value: 1.18e-03
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
3HVZ_C      12 TPKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKV-------DGRIVPIDYKVKTGEIIDVLT 67
Cdd:cd01666 15 PDFDEPFILRRGSTVEDVAEKIHKDLAENFKYARVwgksvkfDGQRVGLDHVLEDGDIVEIHK 77
PRK12444 PRK12444
threonyl-tRNA synthetase; Reviewed
 13-67 6.06e-03

threonyl-tRNA synthetase; Reviewed


Pssm-ID: 183530 [Multi-domain]  Cd Length: 639  Bit Score: 33.57  E-value: 6.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
3HVZ_C        13 PKGDVISLPIGSTVIDFAYAIHSAVGNR*IGAKVDGRIVPIDYKVKTGEIIDVLT 67
Cdd:PRK12444  11 PDGSVKEFVKGITLEEIAGSISSSLKKKAVAGKVNDKLYDLRRNLEEDAEVEIIT 65
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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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