NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2527666054|ref|WP_288659371|]
View 

GTP pyrophosphokinase family protein [uncultured Limosilactobacillus sp.]

Protein Classification

GTP pyrophosphokinase( domain architecture ID 10789386)

GTP pyrophosphokinase functions as a (p)ppGpp synthase, catalyzing the reaction of GTP and ATP to form guanosine 3'-diphosphate 5'-triphosphate and AMP

CATH:  1.10.287.860
EC:  2.7.6.5
Gene Ontology:  GO:0015969|GO:0008728|GO:0005524|GO:0046872|GO:0016310
PubMed:  26460002|33162948|30980074
SCOP:  4001424

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 1-206 3.48e-94

ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport and metabolism, Signal transduction mechanisms];


:

Pssm-ID: 441924 [Multi-domain]  Cd Length: 286  Bit Score: 277.43  E-value: 3.48e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054   1 MIENWQHFLLPYQQAVNELKVKLRGMRKQYQEqGEHSPIEFVTGRVKPIDSIKEKMVRRH--VQEDRLEQDMQDIAGLRI 78
Cdd:COG2357    11 FLADYERFLPPYEAALEELKTKLEILLDEFEK-HGGSPIEHVTSRVKSPESIIEKLRRKGlpLTYENILEEITDIAGIRI 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  79 MCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVIEYPVQLVTGEKKILAEIQVRTLAMNFWATIEHSLN 158
Cdd:COG2357    90 ICYFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLR 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2527666054 159 YKYQGAFPEELSARLQRAAEAAFRLDNEMSEIREEIKEAQTLFSQRTA 206
Cdd:COG2357   170 YKYDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFEDKEA 217
 
Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 1-206 3.48e-94

ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 441924 [Multi-domain]  Cd Length: 286  Bit Score: 277.43  E-value: 3.48e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054   1 MIENWQHFLLPYQQAVNELKVKLRGMRKQYQEqGEHSPIEFVTGRVKPIDSIKEKMVRRH--VQEDRLEQDMQDIAGLRI 78
Cdd:COG2357    11 FLADYERFLPPYEAALEELKTKLEILLDEFEK-HGGSPIEHVTSRVKSPESIIEKLRRKGlpLTYENILEEITDIAGIRI 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  79 MCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVIEYPVQLVTGEKKILAEIQVRTLAMNFWATIEHSLN 158
Cdd:COG2357    90 ICYFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLR 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2527666054 159 YKYQGAFPEELSARLQRAAEAAFRLDNEMSEIREEIKEAQTLFSQRTA 206
Cdd:COG2357   170 YKYDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFEDKEA 217
RelA_SpoT pfam04607
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
 44-163 2.45e-50

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: 159.64  E-value: 2.45e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  44 GRVKPIDSIKEKMVRRHVQEDrleqDMQDIAGLRIMCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVI 123
Cdd:pfam04607   1 GRVKSPYSIYEKMQRKGLLFE----EIYDLIGIRIIVQFVDDCYRVLGIIHSLWDPIPGRFKDYIAIPKPNGYRSLHTTV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2527666054 124 EYpvqlvtGEKKILAEIQVRTLAMNFWAT--IEHSLNYKYQG 163
Cdd:pfam04607  77 II------GPEGVPVEIQIRTIAMHFWAEygIAHHWRYKEGG 112
RelA_SpoT smart00954
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
 44-164 4.14e-45

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: 146.17  E-value: 4.14e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054   44 GRVKPIDSIKEKMVRRHvqeDRLEQDMQDIAGLRIMCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVI 123
Cdd:smart00954   1 GRVKHLYSIYKKMRRKG---EISFDEITDLAGVRIIVDFVDDCYRVLGILHSLFDPIPGRFKDYIANPKPNGYRSLHTTV 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2527666054  124 EYPvqlvtgeKKILAEIQVRTLAMNFWATIEHSLNYKYQGA 164
Cdd:smart00954  78 IGP-------EGRPVEIQIRTILMHAWAELGHAAHYKYKEG 111
NT_Rel-Spo_like cd05399
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
 13-153 9.64e-36

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: 122.84  E-value: 9.64e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  13 QQAVNELKVKLRgmrkqyqEQGEHSPIEFVTGRVKPIDSIKEKMvRRHVQEDRLEQDMQDIAGLRIMCQFVEDIYVVVDL 92
Cdd:cd05399     1 KAALEEIADLLR-------DAGIIGRVASVSGRVKSPYSIYEKL-RRKGKDLPILDEITDLVGVRVVLLFVDDCYRVLDL 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2527666054  93 LRQRSDMTILEERDYVTNVKPSGYRSYHIVIEYPvqlvTGEKKILAEIQVRTLAMNFWATI 153
Cdd:cd05399    73 LHSLFKVIPGRVKDYIAEPKENGYQSLHLVVRGP----EDKAGVLIEIQIRTILMHAWAEL 129
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 23-162 1.43e-08

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 54.41  E-value: 1.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  23 LRGMRKQYQEQGEHSPIefvTGRVKPIDSIKEKMVRRHVQEDRLeqdmQDIAGLRIMCQFVEDIY----VVVDLLRQRSD 98
Cdd:PRK10872  233 VGHLRAEMKAEGVKAEV---YGRPKHIYSIWRKMQKKSLAFDEL----FDVRAVRIVAERLQDCYaalgIVHTHYRHLPD 305

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2527666054  99 mtilEERDYVTNVKPSGYRSYHIVieypvqlVTGEKKILAEIQVRTLAMNFWATIEHSLNYKYQ 162
Cdd:PRK10872  306 ----EFDDYVANPKPNGYQSIHTV-------VLGPGGKTVEIQIRTRQMHEDAELGVAAHWKYK 358
 
Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 1-206 3.48e-94

ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 441924 [Multi-domain]  Cd Length: 286  Bit Score: 277.43  E-value: 3.48e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054   1 MIENWQHFLLPYQQAVNELKVKLRGMRKQYQEqGEHSPIEFVTGRVKPIDSIKEKMVRRH--VQEDRLEQDMQDIAGLRI 78
Cdd:COG2357    11 FLADYERFLPPYEAALEELKTKLEILLDEFEK-HGGSPIEHVTSRVKSPESIIEKLRRKGlpLTYENILEEITDIAGIRI 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  79 MCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVIEYPVQLVTGEKKILAEIQVRTLAMNFWATIEHSLN 158
Cdd:COG2357    90 ICYFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLR 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2527666054 159 YKYQGAFPEELSARLQRAAEAAFRLDNEMSEIREEIKEAQTLFSQRTA 206
Cdd:COG2357   170 YKYDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFEDKEA 217
RelA_SpoT pfam04607
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
 44-163 2.45e-50

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: 159.64  E-value: 2.45e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  44 GRVKPIDSIKEKMVRRHVQEDrleqDMQDIAGLRIMCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVI 123
Cdd:pfam04607   1 GRVKSPYSIYEKMQRKGLLFE----EIYDLIGIRIIVQFVDDCYRVLGIIHSLWDPIPGRFKDYIAIPKPNGYRSLHTTV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2527666054 124 EYpvqlvtGEKKILAEIQVRTLAMNFWAT--IEHSLNYKYQG 163
Cdd:pfam04607  77 II------GPEGVPVEIQIRTIAMHFWAEygIAHHWRYKEGG 112
RelA_SpoT smart00954
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
 44-164 4.14e-45

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: 146.17  E-value: 4.14e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054   44 GRVKPIDSIKEKMVRRHvqeDRLEQDMQDIAGLRIMCQFVEDIYVVVDLLRQRSDMTILEERDYVTNVKPSGYRSYHIVI 123
Cdd:smart00954   1 GRVKHLYSIYKKMRRKG---EISFDEITDLAGVRIIVDFVDDCYRVLGILHSLFDPIPGRFKDYIANPKPNGYRSLHTTV 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2527666054  124 EYPvqlvtgeKKILAEIQVRTLAMNFWATIEHSLNYKYQGA 164
Cdd:smart00954  78 IGP-------EGRPVEIQIRTILMHAWAELGHAAHYKYKEG 111
NT_Rel-Spo_like cd05399
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
 13-153 9.64e-36

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: 122.84  E-value: 9.64e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  13 QQAVNELKVKLRgmrkqyqEQGEHSPIEFVTGRVKPIDSIKEKMvRRHVQEDRLEQDMQDIAGLRIMCQFVEDIYVVVDL 92
Cdd:cd05399     1 KAALEEIADLLR-------DAGIIGRVASVSGRVKSPYSIYEKL-RRKGKDLPILDEITDLVGVRVVLLFVDDCYRVLDL 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2527666054  93 LRQRSDMTILEERDYVTNVKPSGYRSYHIVIEYPvqlvTGEKKILAEIQVRTLAMNFWATI 153
Cdd:cd05399    73 LHSLFKVIPGRVKDYIAEPKENGYQSLHLVVRGP----EDKAGVLIEIQIRTILMHAWAEL 129
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 23-162 1.43e-08

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 54.41  E-value: 1.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  23 LRGMRKQYQEQGEHSPIefvTGRVKPIDSIKEKMVRRHVQEDRLeqdmQDIAGLRIMCQFVEDIY----VVVDLLRQRSD 98
Cdd:PRK10872  233 VGHLRAEMKAEGVKAEV---YGRPKHIYSIWRKMQKKSLAFDEL----FDVRAVRIVAERLQDCYaalgIVHTHYRHLPD 305

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2527666054  99 mtilEERDYVTNVKPSGYRSYHIVieypvqlVTGEKKILAEIQVRTLAMNFWATIEHSLNYKYQ 162
Cdd:PRK10872  306 ----EFDDYVANPKPNGYQSIHTV-------VLGPGGKTVEIQIRTRQMHEDAELGVAAHWKYK 358
SpoT COG0317
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];
13-148 2.66e-08

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


Pssm-ID: 440086 [Multi-domain]  Cd Length: 722  Bit Score: 53.62  E-value: 2.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527666054  13 QQAVNELKVKLRgmrkqyqEQGehspIEF-VTGRVKPIDSIKEKMVRRHVQedrLEQdMQDIAGLRIMCQFVEDIYVVVD 91
Cdd:COG0317   223 EEIIEELKEELA-------EAG----IKAeVSGRPKHIYSIYRKMQRKGLS---FEE-IYDLYAFRIIVDTVDDCYAALG 287

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2527666054  92 LLRQRsdMTILEER--DYVTNVKPSGYRSYHIVieypvqlVTGEKKILAEIQVRTLAMN 148
Cdd:COG0317   288 IVHSL--WKPIPGRfkDYIAIPKPNGYQSLHTT-------VIGPDGKPVEVQIRTEEMH 337
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH