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Conserved domains on  [gi|490248452|ref|WP_004146573|]
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GTP-binding protein, partial [Klebsiella pneumoniae]

Protein Classification

chaper_GTP_ZigA superfamily-containing protein( domain architecture ID 1904169)

chaper_GTP_ZigA superfamily-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
chaper_GTP_ZigA super family cl45739
zinc metallochaperone GTPase ZigA; The GTPase ZigA (Zur-induced GTPase A) is a zinc ...
 1-172 2.56e-130

zinc metallochaperone GTPase ZigA; The GTPase ZigA (Zur-induced GTPase A) is a zinc metallochaperone thought to be important for histidine utilization (HUT), supplying Zn to the histidine ammonia-lyase HutH when required under low-Zn conditions.


The actual alignment was detected with superfamily member NF038288:

Pssm-ID: 468453 [Multi-domain]  Cd Length: 390  Bit Score: 370.26  E-value: 2.56e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYGSEDSIQSRGESLGEGDERSVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:NF038288 129 MVTVVDAVNFLRDYDSADSLQERGESLGEEDERTVVDLLVDQVEFADVILLNKTDLVSEAELERLTAILRSLNPRARIVP 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452  81 SQFGQVPLSNIRNTGLFDFEQAAQAPGWLKELRGEHTPETEEYGITSFVFRARRPFHPTRFWQVMENELDG-VVRSKGYF 159
Cdd:NF038288 209 ISFGQVPLDKVLNTGLFDFERAAQAPGWLKELRGEHTPETEEYGISSFVYRARRPFHPQRFYDFLHSEWPGkVLRSKGFF 288

                        170
                 ....*....|...
gi 490248452 160 WLASRPEFAGSWS 172
Cdd:NF038288 289 WLASRPDFAGSWS 301
 
Name Accession Description Interval E-value
chaper_GTP_ZigA NF038288
zinc metallochaperone GTPase ZigA; The GTPase ZigA (Zur-induced GTPase A) is a zinc ...
 1-172 2.56e-130

zinc metallochaperone GTPase ZigA; The GTPase ZigA (Zur-induced GTPase A) is a zinc metallochaperone thought to be important for histidine utilization (HUT), supplying Zn to the histidine ammonia-lyase HutH when required under low-Zn conditions.


Pssm-ID: 468453 [Multi-domain]  Cd Length: 390  Bit Score: 370.26  E-value: 2.56e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYGSEDSIQSRGESLGEGDERSVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:NF038288 129 MVTVVDAVNFLRDYDSADSLQERGESLGEEDERTVVDLLVDQVEFADVILLNKTDLVSEAELERLTAILRSLNPRARIVP 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452  81 SQFGQVPLSNIRNTGLFDFEQAAQAPGWLKELRGEHTPETEEYGITSFVFRARRPFHPTRFWQVMENELDG-VVRSKGYF 159
Cdd:NF038288 209 ISFGQVPLDKVLNTGLFDFERAAQAPGWLKELRGEHTPETEEYGISSFVYRARRPFHPQRFYDFLHSEWPGkVLRSKGFF 288

                        170
                 ....*....|...
gi 490248452 160 WLASRPEFAGSWS 172
Cdd:NF038288 289 WLASRPDFAGSWS 301
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
 1-165 5.04e-64

Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction only];


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 199.24  E-value: 5.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYgsedsiqsrgeslgegDERSVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:COG0523  121 VVTVVDARNLLDDL----------------ADRTLHELLVDQIAFADVIVLNKTDLVDEEELAALEARLRALNPGAPIVR 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452  81 SQFGQVPLSNIRNTGLFDFEQAAQAPGWLKELRG-EHTpeteeYGITSFVFRARRPFHPTRFWQVMENELDGVVRSKGYF 159
Cdd:COG0523  185 TSHGEVDPALLLDLGLFDLEAALARPGWLEELRDhEHD-----DGIRSFVFRSDRPFDPERLADFLEELGPGVLRAKGFL 259


                 ....*.
gi 490248452 160 WLASRP 165
Cdd:COG0523  260 WLAGRP 265
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
 1-95 3.92e-28

cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.


Pssm-ID: 349766  Cd Length: 198  Bit Score: 103.37  E-value: 3.92e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYGSEDsiqsrgeslgegdersVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:cd03112  120 VVTVVDAKNFLKQLDEED----------------VSDLAVDQIAFADVIVLNKTDLVDEEELEALRARIRALNPGAKIVE 183

                         90
                 ....*....|....*
gi 490248452  81 SQFGQVPLSNIRNTG 95
Cdd:cd03112  184 TTYGRVDLEELLGTG 198
CobW_C smart00833
Cobalamin synthesis protein cobW C-terminal domain; CobW proteins are generally found proximal ...
 125-172 1.59e-18

Cobalamin synthesis protein cobW C-terminal domain; CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression.


Pssm-ID: 214844 [Multi-domain]  Cd Length: 92  Bit Score: 75.71  E-value: 1.59e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 490248452   125 ITSFVFRARRPFHPTRFWQVMENELDGVVRSKGYFWLASRPEFAGSWS 172
Cdd:smart00833   1 ISSFVYRARRPFHPQRLLAALDELPEGVLRAKGFFWLASRPDLPGVLS 48
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
 1-79 5.11e-13

CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.


Pssm-ID: 396860  Cd Length: 179  Bit Score: 63.43  E-value: 5.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452    1 MVTVVDAYNflkdygsedsiqsrgeslgEGDERSVVDLLIDQIEFCDVLVLNKVDLIS-EAKKEKLVAILRSLNPRARIV 79
Cdd:pfam02492 118 VITVVDAAN-------------------EADGEKIPRKAGDQIAFADLIVLNKTDLAPeVALLEVLEEDLRRLNPGAPVV 178
 
Name Accession Description Interval E-value
chaper_GTP_ZigA NF038288
zinc metallochaperone GTPase ZigA; The GTPase ZigA (Zur-induced GTPase A) is a zinc ...
 1-172 2.56e-130

zinc metallochaperone GTPase ZigA; The GTPase ZigA (Zur-induced GTPase A) is a zinc metallochaperone thought to be important for histidine utilization (HUT), supplying Zn to the histidine ammonia-lyase HutH when required under low-Zn conditions.


Pssm-ID: 468453 [Multi-domain]  Cd Length: 390  Bit Score: 370.26  E-value: 2.56e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYGSEDSIQSRGESLGEGDERSVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:NF038288 129 MVTVVDAVNFLRDYDSADSLQERGESLGEEDERTVVDLLVDQVEFADVILLNKTDLVSEAELERLTAILRSLNPRARIVP 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452  81 SQFGQVPLSNIRNTGLFDFEQAAQAPGWLKELRGEHTPETEEYGITSFVFRARRPFHPTRFWQVMENELDG-VVRSKGYF 159
Cdd:NF038288 209 ISFGQVPLDKVLNTGLFDFERAAQAPGWLKELRGEHTPETEEYGISSFVYRARRPFHPQRFYDFLHSEWPGkVLRSKGFF 288

                        170
                 ....*....|...
gi 490248452 160 WLASRPEFAGSWS 172
Cdd:NF038288 289 WLASRPDFAGSWS 301
YejR COG0523
Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction ...
 1-165 5.04e-64

Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction only];


Pssm-ID: 440289 [Multi-domain]  Cd Length: 318  Bit Score: 199.24  E-value: 5.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYgsedsiqsrgeslgegDERSVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:COG0523  121 VVTVVDARNLLDDL----------------ADRTLHELLVDQIAFADVIVLNKTDLVDEEELAALEARLRALNPGAPIVR 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452  81 SQFGQVPLSNIRNTGLFDFEQAAQAPGWLKELRG-EHTpeteeYGITSFVFRARRPFHPTRFWQVMENELDGVVRSKGYF 159
Cdd:COG0523  185 TSHGEVDPALLLDLGLFDLEAALARPGWLEELRDhEHD-----DGIRSFVFRSDRPFDPERLADFLEELGPGVLRAKGFL 259


                 ....*.
gi 490248452 160 WLASRP 165
Cdd:COG0523  260 WLAGRP 265
CobW-like cd03112
cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino ...
 1-95 3.92e-28

cobalamin synthesis protein CobW; The function of this protein family is unknown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.


Pssm-ID: 349766  Cd Length: 198  Bit Score: 103.37  E-value: 3.92e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452   1 MVTVVDAYNFLKDYGSEDsiqsrgeslgegdersVVDLLIDQIEFCDVLVLNKVDLISEAKKEKLVAILRSLNPRARIVV 80
Cdd:cd03112  120 VVTVVDAKNFLKQLDEED----------------VSDLAVDQIAFADVIVLNKTDLVDEEELEALRARIRALNPGAKIVE 183

                         90
                 ....*....|....*
gi 490248452  81 SQFGQVPLSNIRNTG 95
Cdd:cd03112  184 TTYGRVDLEELLGTG 198
CobW_C smart00833
Cobalamin synthesis protein cobW C-terminal domain; CobW proteins are generally found proximal ...
 125-172 1.59e-18

Cobalamin synthesis protein cobW C-terminal domain; CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression.


Pssm-ID: 214844 [Multi-domain]  Cd Length: 92  Bit Score: 75.71  E-value: 1.59e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 490248452   125 ITSFVFRARRPFHPTRFWQVMENELDGVVRSKGYFWLASRPEFAGSWS 172
Cdd:smart00833   1 ISSFVYRARRPFHPQRLLAALDELPEGVLRAKGFFWLASRPDLPGVLS 48
cobW pfam02492
CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase ...
 1-79 5.11e-13

CobW/HypB/UreG, nucleotide-binding domain; This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.


Pssm-ID: 396860  Cd Length: 179  Bit Score: 63.43  E-value: 5.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490248452    1 MVTVVDAYNflkdygsedsiqsrgeslgEGDERSVVDLLIDQIEFCDVLVLNKVDLIS-EAKKEKLVAILRSLNPRARIV 79
Cdd:pfam02492 118 VITVVDAAN-------------------EADGEKIPRKAGDQIAFADLIVLNKTDLAPeVALLEVLEEDLRRLNPGAPVV 178
CobW_C pfam07683
Cobalamin synthesis protein cobW C-terminal domain; This is a large and diverse family of ...
 125-165 1.48e-12

Cobalamin synthesis protein cobW C-terminal domain; This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family.


Pssm-ID: 462228 [Multi-domain]  Cd Length: 93  Bit Score: 60.33  E-value: 1.48e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 490248452  125 ITSFVFRARRPFHPTRFWQVMENEL--DGVVRSKGYFWLASRP 165
Cdd:pfam07683   1 ISSFVFRADRPFDPERLEAWLEDLLlpEGILRAKGILWLAGRP 43
YjiA COG2403
Zn/Ni/Co-binding GTPase YjiA, predicted metallochaperone, CobW/Nha3/YciC family [Inorganic ion ...
 46-79 8.75e-04

Zn/Ni/Co-binding GTPase YjiA, predicted metallochaperone, CobW/Nha3/YciC family [Inorganic ion transport and metabolism];


Pssm-ID: 441959  Cd Length: 441  Bit Score: 38.67  E-value: 8.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 490248452  46 CDVLVLNKVDLISEAKKEKLVAILRSLNPRARIV 79
Cdd:COG2403  262 ADVVVINKVDTADPEDIETVRENIRKVNPKAEII 295
Era COG1159
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];
24-96 1.40e-03

GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440773 [Multi-domain]  Cd Length: 290  Bit Score: 38.05  E-value: 1.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490248452  24 GESLGEGDERsvvdlLIDQIEFCD---VLVLNKVDLISEAKKEKLVAILRSLNPRARIvvsqfgqVPLSNIRNTGL 96
Cdd:COG1159   93 TEKIGEGDEF-----ILELLKKLKtpvILVINKIDLVKKEELLPLLAEYSELLDFAEI-------VPISALKGDNV 156
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 25-81 5.79e-03

E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.


Pssm-ID: 206726 [Multi-domain]  Cd Length: 168  Bit Score: 35.51  E-value: 5.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490248452  25 ESLGEGDERsVVDLLIDQIEFCdVLVLNKVDLISEAKK-EKLVAILRSLNPRARIV-VS 81
Cdd:cd04163   94 EWIGEGDEF-ILELLKKSKTPV-ILVLNKIDLVKDKEDlLPLLEKLKELHPFAEIFpIS 150
HypB cd05390
nickel incorporation protein HypB; HypB is one of numerous accessory proteins required for the ...
 46-79 7.12e-03

nickel incorporation protein HypB; HypB is one of numerous accessory proteins required for the maturation of nickel-dependent hydrogenases, like carbon monoxide dehydrogenase or urease. HypB is a GTP-binding protein and has GTP hyrolase activity. It forms homodimer and is capable of binding two nickel ions and two zinc ions. The active site is located on the dimer interface. Energy from hydrolysis of GTP is used to insert nickels into hydrogenases.


Pssm-ID: 349775  Cd Length: 203  Bit Score: 35.65  E-value: 7.12e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490248452  46 CDVLVLNKVDLIS--EAKKEKLVAILRSLNPRARIV 79
Cdd:cd05390  149 ADVVLINKIDLLPyfDFDVEKAKEDIKKLNPNAPII 184
 
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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