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Conserved domains on  [gi|518364744|ref|WP_019534951|]
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GTP pyrophosphokinase family protein [Paenibacillus ginsengihumi]

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

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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 ...
 4-264 1.43e-90

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: 269.72  E-value: 1.43e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744   4 RDWKLFLQPYEQTVEELKVKFKTLRAELKnREEYSPIEFVTGRVKRISSIIEKMKRLNVPM--ENIETGIEDIAGIRIMC 81
Cdd:COG2357   13 ADYERFLPPYEAALEELKTKLEILLDEFE-KHGGSPIEHVTSRVKSPESIIEKLRRKGLPLtyENILEEITDIAGIRIIC 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  82 QFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIVEYPVQTALGMKRVLAEIQLRTLAMNFWATIEHSLNYK 161
Cdd:COG2357   92 YFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLRYK 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744 162 YREKLPEQVVERLSRAAEAAYLLDREMSSIRDEIMEAQKLFEDKSRIVSQVLSGIQRLYYFHRVREAAQFQMRFNELWDI 241
Cdd:COG2357  172 YDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFEDKEAIAEESLAALLLLLEDLGVDLDFILAIELSELFLL 251

                        250       260
                 ....*....|....*....|...
gi 518364744 242 DDVWHFKELLHDIEEAIRRAAAK 264
Cdd:COG2357  252 DLELELAKLLRIAEEIAILRLLD 274
 
Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 4-264 1.43e-90

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: 269.72  E-value: 1.43e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744   4 RDWKLFLQPYEQTVEELKVKFKTLRAELKnREEYSPIEFVTGRVKRISSIIEKMKRLNVPM--ENIETGIEDIAGIRIMC 81
Cdd:COG2357   13 ADYERFLPPYEAALEELKTKLEILLDEFE-KHGGSPIEHVTSRVKSPESIIEKLRRKGLPLtyENILEEITDIAGIRIIC 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  82 QFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIVEYPVQTALGMKRVLAEIQLRTLAMNFWATIEHSLNYK 161
Cdd:COG2357   92 YFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLRYK 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744 162 YREKLPEQVVERLSRAAEAAYLLDREMSSIRDEIMEAQKLFEDKSRIVSQVLSGIQRLYYFHRVREAAQFQMRFNELWDI 241
Cdd:COG2357  172 YDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFEDKEAIAEESLAALLLLLEDLGVDLDFILAIELSELFLL 251

                        250       260
                 ....*....|....*....|...
gi 518364744 242 DDVWHFKELLHDIEEAIRRAAAK 264
Cdd:COG2357  252 DLELELAKLLRIAEEIAILRLLD 274
RelA_SpoT pfam04607
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
 45-165 1.47e-44

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: 146.15  E-value: 1.47e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744   45 GRVKRISSIIEKMKRLNVPMENIEtgieDIAGIRIMCQFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIV 124
Cdd:pfam04607   1 GRVKSPYSIYEKMQRKGLLFEEIY----DLIGIRIIVQFVDDCYRVLGIIHSLWDPIPGRFKDYIAIPKPNGYRSLHTTV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 518364744  125 EYpvqtalGMKRVLAEIQLRTLAMNFWAT--IEHSLNYKYREK 165
Cdd:pfam04607  77 II------GPEGVPVEIQIRTIAMHFWAEygIAHHWRYKEGGD 113
RelA_SpoT smart00954
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
 45-164 9.30e-41

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: 136.16  E-value: 9.30e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744    45 GRVKRISSIIEKMKRLNvpmENIETGIEDIAGIRIMCQFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIV 124
Cdd:smart00954   1 GRVKHLYSIYKKMRRKG---EISFDEITDLAGVRIIVDFVDDCYRVLGILHSLFDPIPGRFKDYIANPKPNGYRSLHTTV 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 518364744   125 EYPVQTalgmkrvLAEIQLRTLAMNFWATIEHSLNYKYRE 164
Cdd:smart00954  78 IGPEGR-------PVEIQIRTILMHAWAELGHAAHYKYKE 110
NT_Rel-Spo_like cd05399
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
 26-154 1.02e-32

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: 116.29  E-value: 1.02e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  26 TLRAELKNREEYSPIEFVTGRVKRISSIIEKMKRLNvPMENIETGIEDIAGIRIMCQFVEDIEALAELIRAREDMTVKYV 105
Cdd:cd05399    6 EIADLLRDAGIIGRVASVSGRVKSPYSIYEKLRRKG-KDLPILDEITDLVGVRVVLLFVDDCYRVLDLLHSLFKVIPGRV 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 518364744 106 KDYVTNKKPSGYRSYHIIVEYPVqtalGMKRVLAEIQLRTLAMNFWATI 154
Cdd:cd05399   85 KDYIAEPKENGYQSLHLVVRGPE----DKAGVLIEIQIRTILMHAWAEL 129
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 14-164 1.38e-07

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 52.10  E-value: 1.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  14 EQTVEELkvkFKTLRAELKnrEEYSPIEfVTGRVKRISSIIEKMKRLNVPMENIEtgieDIAGIRIMCQFVEDIEALAEL 93
Cdd:PRK10872 226 EHYIEEF---VGHLRAEMK--AEGVKAE-VYGRPKHIYSIWRKMQKKSLAFDELF----DVRAVRIVAERLQDCYAALGI 295

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518364744  94 IRAREDMTVKYVKDYVTNKKPSGYRSYHIIVeypvqtaLGMKRVLAEIQLRTLAMNFWATIEHSLNYKYRE 164
Cdd:PRK10872 296 VHTHYRHLPDEFDDYVANPKPNGYQSIHTVV-------LGPGGKTVEIQIRTRQMHEDAELGVAAHWKYKE 359
 
Name Accession Description Interval E-value
YjbM COG2357
ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport ...
 4-264 1.43e-90

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: 269.72  E-value: 1.43e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744   4 RDWKLFLQPYEQTVEELKVKFKTLRAELKnREEYSPIEFVTGRVKRISSIIEKMKRLNVPM--ENIETGIEDIAGIRIMC 81
Cdd:COG2357   13 ADYERFLPPYEAALEELKTKLEILLDEFE-KHGGSPIEHVTSRVKSPESIIEKLRRKGLPLtyENILEEITDIAGIRIIC 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  82 QFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIVEYPVQTALGMKRVLAEIQLRTLAMNFWATIEHSLNYK 161
Cdd:COG2357   92 YFVDDIYRVAELLRSQFDVKIIEEKDYIKNPKPNGYRSLHLIVRVPVFLSDGPKGVPVEIQIRTIAMDFWAELEHKLRYK 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744 162 YREKLPEQVVERLSRAAEAAYLLDREMSSIRDEIMEAQKLFEDKSRIVSQVLSGIQRLYYFHRVREAAQFQMRFNELWDI 241
Cdd:COG2357  172 YDGEIPEEIKRRLKRAAALLELLDEEMSEIRDEIEEAQKEFEDKEAIAEESLAALLLLLEDLGVDLDFILAIELSELFLL 251

                        250       260
                 ....*....|....*....|...
gi 518364744 242 DDVWHFKELLHDIEEAIRRAAAK 264
Cdd:COG2357  252 DLELELAKLLRIAEEIAILRLLD 274
RelA_SpoT pfam04607
Region found in RelA / SpoT proteins; This region of unknown function is found in RelA and ...
 45-165 1.47e-44

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: 146.15  E-value: 1.47e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744   45 GRVKRISSIIEKMKRLNVPMENIEtgieDIAGIRIMCQFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIV 124
Cdd:pfam04607   1 GRVKSPYSIYEKMQRKGLLFEEIY----DLIGIRIIVQFVDDCYRVLGIIHSLWDPIPGRFKDYIAIPKPNGYRSLHTTV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 518364744  125 EYpvqtalGMKRVLAEIQLRTLAMNFWAT--IEHSLNYKYREK 165
Cdd:pfam04607  77 II------GPEGVPVEIQIRTIAMHFWAEygIAHHWRYKEGGD 113
RelA_SpoT smart00954
Region found in RelA / SpoT proteins; The functions of Escherichia coli RelA and SpoT differ ...
 45-164 9.30e-41

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: 136.16  E-value: 9.30e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744    45 GRVKRISSIIEKMKRLNvpmENIETGIEDIAGIRIMCQFVEDIEALAELIRAREDMTVKYVKDYVTNKKPSGYRSYHIIV 124
Cdd:smart00954   1 GRVKHLYSIYKKMRRKG---EISFDEITDLAGVRIIVDFVDDCYRVLGILHSLFDPIPGRFKDYIANPKPNGYRSLHTTV 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 518364744   125 EYPVQTalgmkrvLAEIQLRTLAMNFWATIEHSLNYKYRE 164
Cdd:smart00954  78 IGPEGR-------PVEIQIRTILMHAWAELGHAAHYKYKE 110
NT_Rel-Spo_like cd05399
Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; ...
 26-154 1.02e-32

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: 116.29  E-value: 1.02e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  26 TLRAELKNREEYSPIEFVTGRVKRISSIIEKMKRLNvPMENIETGIEDIAGIRIMCQFVEDIEALAELIRAREDMTVKYV 105
Cdd:cd05399    6 EIADLLRDAGIIGRVASVSGRVKSPYSIYEKLRRKG-KDLPILDEITDLVGVRVVLLFVDDCYRVLDLLHSLFKVIPGRV 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 518364744 106 KDYVTNKKPSGYRSYHIIVEYPVqtalGMKRVLAEIQLRTLAMNFWATI 154
Cdd:cd05399   85 KDYIAEPKENGYQSLHLVVRGPE----DKAGVLIEIQIRTILMHAWAEL 129
SpoT COG0317
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription];
25-149 2.18e-08

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


Pssm-ID: 440086 [Multi-domain]  Cd Length: 722  Bit Score: 54.39  E-value: 2.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  25 KTLRAELKNREeyspIEF-VTGRVKRISSIIEKMKRLNVPMENietgIEDIAGIRIMcqfVEDIE----ALAEL------ 93
Cdd:COG0317  227 EELKEELAEAG----IKAeVSGRPKHIYSIYRKMQRKGLSFEE----IYDLYAFRII---VDTVDdcyaALGIVhslwkp 295

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 518364744  94 IRARedmtvkyVKDYVTNKKPSGYRSYHIIVeypvqtaLGMKRVLAEIQLRTLAMN 149
Cdd:COG0317  296 IPGR-------FKDYIAIPKPNGYQSLHTTV-------IGPDGKPVEVQIRTEEMH 337
relA PRK10872
(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
 14-164 1.38e-07

(p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional


Pssm-ID: 182797 [Multi-domain]  Cd Length: 743  Bit Score: 52.10  E-value: 1.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518364744  14 EQTVEELkvkFKTLRAELKnrEEYSPIEfVTGRVKRISSIIEKMKRLNVPMENIEtgieDIAGIRIMCQFVEDIEALAEL 93
Cdd:PRK10872 226 EHYIEEF---VGHLRAEMK--AEGVKAE-VYGRPKHIYSIWRKMQKKSLAFDELF----DVRAVRIVAERLQDCYAALGI 295

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518364744  94 IRAREDMTVKYVKDYVTNKKPSGYRSYHIIVeypvqtaLGMKRVLAEIQLRTLAMNFWATIEHSLNYKYRE 164
Cdd:PRK10872 296 VHTHYRHLPDEFDDYVANPKPNGYQSIHTVV-------LGPGGKTVEIQIRTRQMHEDAELGVAAHWKYKE 359
 
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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