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Conserved domains on  [gi|513036022|gb|AGO08418|]
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GTP pyrophosphokinase [Lactiplantibacillus plantarum 16]

Protein Classification

GTP pyrophosphokinase family protein( domain architecture ID 10789386)

GTP pyrophosphokinase family protein similar to Bacillus subtilis GTP pyrophosphokinases, YwaC and YjbM

Gene Ontology:  GO:0015969

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 1-201 5.94e-97

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: 283.98  E-value: 5.94e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022   1 MEDWNHFLLPYQQAVDELKVKLRGMRKQFRdLNQHEPIEFVTGRVKPVDSIKEKMTRR--KVQEDRLEQDMQDIAGLRIM 78
Cdd:COG2357   12 LADYERFLPPYEAALEELKTKLEILLDEFE-KHGGSPIEHVTSRVKSPESIIEKLRRKglPLTYENILEEITDIAGIRII 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  79 CQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVIEYPVQMVGGEKKILAEIQVRTLAMNFWATIEHSLNY 158
Cdd:COG2357   91 CYFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLRY 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 513036022 159 KYQGDFPENLSQRLQRAAEAAFSLDKEMSEIREEIQEAQSLFS 201
Cdd:COG2357  171 KYDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFE 213
 
Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 1-201 5.94e-97

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: 283.98  E-value: 5.94e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022   1 MEDWNHFLLPYQQAVDELKVKLRGMRKQFRdLNQHEPIEFVTGRVKPVDSIKEKMTRR--KVQEDRLEQDMQDIAGLRIM 78
Cdd:COG2357   12 LADYERFLPPYEAALEELKTKLEILLDEFE-KHGGSPIEHVTSRVKSPESIIEKLRRKglPLTYENILEEITDIAGIRII 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  79 CQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVIEYPVQMVGGEKKILAEIQVRTLAMNFWATIEHSLNY 158
Cdd:COG2357   91 CYFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLRY 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 513036022 159 KYQGDFPENLSQRLQRAAEAAFSLDKEMSEIREEIQEAQSLFS 201
Cdd:COG2357  171 KYDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFE 213
RelA_SpoT pfam04607
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
 43-163 3.54e-51

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: 161.56  E-value: 3.54e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022   43 GRVKPVDSIKEKMTRRKVQEDrleqDMQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVI 122
Cdd:pfam04607   1 GRVKSPYSIYEKMQRKGLLFE----EIYDLIGIRIIVQFVDDCYRVLGIIHSLWDPIPGRFKDYIAIPKPNGYRSLHTTV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 513036022  123 EYpvqmvgGEKKILAEIQVRTLAMNFWAT--IEHSLNYKYQGD 163
Cdd:pfam04607  77 II------GPEGVPVEIQIRTIAMHFWAEygIAHHWRYKEGGD 113
RelA_SpoT smart00954
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
 43-163 1.04e-47

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: 152.34  E-value: 1.04e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022    43 GRVKPVDSIKEKMTRRkvqEDRLEQDMQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVI 122
Cdd:smart00954   1 GRVKHLYSIYKKMRRK---GEISFDEITDLAGVRIIVDFVDDCYRVLGILHSLFDPIPGRFKDYIANPKPNGYRSLHTTV 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 513036022   123 EYPvqmvggeKKILAEIQVRTLAMNFWATIEHSLNYKYQGD 163
Cdd:smart00954  78 IGP-------EGRPVEIQIRTILMHAWAELGHAAHYKYKEG 111
NT_Rel-Spo_like cd05399
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
 25-152 1.82e-38

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: 129.77  E-value: 1.82e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  25 MRKQFRDLNQHEPIEFVTGRVKPVDSIKEKMtRRKVQEDRLEQDMQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEER 104
Cdd:cd05399    7 IADLLRDAGIIGRVASVSGRVKSPYSIYEKL-RRKGKDLPILDEITDLVGVRVVLLFVDDCYRVLDLLHSLFKVIPGRVK 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 513036022 105 DYISNEKPSGYRSYHIVIEYPvqmvGGEKKILAEIQVRTLAMNFWATI 152
Cdd:cd05399   86 DYIAEPKENGYQSLHLVVRGP----EDKAGVLIEIQIRTILMHAWAEL 129
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 41-161 5.24e-07

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 49.40  E-value: 5.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  41 VTGRVKPVDSIKEKMTRRKVQEDRLeqdmQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHI 120
Cdd:PRK10872 249 VYGRPKHIYSIWRKMQKKSLAFDEL----FDVRAVRIVAERLQDCYAALGIVHTHYRHLPDEFDDYVANPKPNGYQSIHT 324

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 513036022 121 VIeypvqmVGGEKKILaEIQVRTLAMNFWATIEHSLNYKYQ 161
Cdd:PRK10872 325 VV------LGPGGKTV-EIQIRTRQMHEDAELGVAAHWKYK 358
 
Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 1-201 5.94e-97

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: 283.98  E-value: 5.94e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022   1 MEDWNHFLLPYQQAVDELKVKLRGMRKQFRdLNQHEPIEFVTGRVKPVDSIKEKMTRR--KVQEDRLEQDMQDIAGLRIM 78
Cdd:COG2357   12 LADYERFLPPYEAALEELKTKLEILLDEFE-KHGGSPIEHVTSRVKSPESIIEKLRRKglPLTYENILEEITDIAGIRII 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  79 CQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVIEYPVQMVGGEKKILAEIQVRTLAMNFWATIEHSLNY 158
Cdd:COG2357   91 CYFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLRY 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 513036022 159 KYQGDFPENLSQRLQRAAEAAFSLDKEMSEIREEIQEAQSLFS 201
Cdd:COG2357  171 KYDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFE 213
RelA_SpoT pfam04607
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
 43-163 3.54e-51

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: 161.56  E-value: 3.54e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022   43 GRVKPVDSIKEKMTRRKVQEDrleqDMQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVI 122
Cdd:pfam04607   1 GRVKSPYSIYEKMQRKGLLFE----EIYDLIGIRIIVQFVDDCYRVLGIIHSLWDPIPGRFKDYIAIPKPNGYRSLHTTV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 513036022  123 EYpvqmvgGEKKILAEIQVRTLAMNFWAT--IEHSLNYKYQGD 163
Cdd:pfam04607  77 II------GPEGVPVEIQIRTIAMHFWAEygIAHHWRYKEGGD 113
RelA_SpoT smart00954
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
 43-163 1.04e-47

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: 152.34  E-value: 1.04e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022    43 GRVKPVDSIKEKMTRRkvqEDRLEQDMQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHIVI 122
Cdd:smart00954   1 GRVKHLYSIYKKMRRK---GEISFDEITDLAGVRIIVDFVDDCYRVLGILHSLFDPIPGRFKDYIANPKPNGYRSLHTTV 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 513036022   123 EYPvqmvggeKKILAEIQVRTLAMNFWATIEHSLNYKYQGD 163
Cdd:smart00954  78 IGP-------EGRPVEIQIRTILMHAWAELGHAAHYKYKEG 111
NT_Rel-Spo_like cd05399
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
 25-152 1.82e-38

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: 129.77  E-value: 1.82e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  25 MRKQFRDLNQHEPIEFVTGRVKPVDSIKEKMtRRKVQEDRLEQDMQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEER 104
Cdd:cd05399    7 IADLLRDAGIIGRVASVSGRVKSPYSIYEKL-RRKGKDLPILDEITDLVGVRVVLLFVDDCYRVLDLLHSLFKVIPGRVK 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 513036022 105 DYISNEKPSGYRSYHIVIEYPvqmvGGEKKILAEIQVRTLAMNFWATI 152
Cdd:cd05399   86 DYIAEPKENGYQSLHLVVRGP----EDKAGVLIEIQIRTILMHAWAEL 129
SpoT COG0317
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];
12-147 1.44e-10

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


Pssm-ID: 440086 [Multi-domain]  Cd Length: 722  Bit Score: 60.17  E-value: 1.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  12 QQAVDELKVKLRGMRKQFRD-----LNQHEpIEF-VTGRVKPVDSIKEKMTRRKVQedrLEQdMQDIAGLRIMCQFVEDI 85
Cdd:COG0317  208 AKLLKEKRGEREEYIEEIIEelkeeLAEAG-IKAeVSGRPKHIYSIYRKMQRKGLS---FEE-IYDLYAFRIIVDTVDDC 282

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 513036022  86 YQVVDLLrkrTDM-TILEER--DYISNEKPSGYRSYHIVIeypvqmVGGEKKILaEIQVRTLAMN 147
Cdd:COG0317  283 YAALGIV---HSLwKPIPGRfkDYIAIPKPNGYQSLHTTV------IGPDGKPV-EVQIRTEEMH 337
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 41-161 5.24e-07

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 49.40  E-value: 5.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513036022  41 VTGRVKPVDSIKEKMTRRKVQEDRLeqdmQDIAGLRIMCQFVEDIYQVVDLLRKRTDMTILEERDYISNEKPSGYRSYHI 120
Cdd:PRK10872 249 VYGRPKHIYSIWRKMQKKSLAFDEL----FDVRAVRIVAERLQDCYAALGIVHTHYRHLPDEFDDYVANPKPNGYQSIHT 324

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 513036022 121 VIeypvqmVGGEKKILaEIQVRTLAMNFWATIEHSLNYKYQ 161
Cdd:PRK10872 325 VV------LGPGGKTV-EIQIRTRQMHEDAELGVAAHWKYK 358
 
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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