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Conserved domains on  [gi|503994069|ref|WP_014228063|]
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MULTISPECIES: HutD family protein [Klebsiella]

Protein Classification

HutD family protein( domain architecture ID 10007956)

HutD family protein similar to Pseudomonas fluorescens histidine utilization protein HutD

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
1-185 4.70e-65

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


:

Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 198.26  E-value: 4.70e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   1 MIRLLPAGLYTEMPWKNGQGMTREVARYPEAGEY---DWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRS- 76
Cdd:COG3758    2 SMRILRAADLPRMPWKNGGGETREIARFPEGAGLddfDWRLSIATVAQDGPFSAFPGIDRTITLLEGDGLRLTVDGQGEh 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069  77 ALIAPFQALGFNGASGVSCEIVGGPLLDFNVIYREAALRATVSWC---GAGTWSHQGGLRILFNAGPALRVSVGDQRYLL 153
Cdd:COG3758   82 TLDEPFQPFAFSGDAPVSARLLGGPVRDFNLMTRRGRARARVRVLrlaGTLPLHADAGTGLLYVLAGAWTVALGGEAITL 161

                        170       180       190
                 ....*....|....*....|....*....|....
gi 503994069 154 EHYDSLLVDEAVAL--VIPDSPGARLARITLIPL 185
Cdd:COG3758  162 EAGDTLLLEAPAPLltLTPLSGDGRLLLVELTPR 195
 
Name Accession Description Interval E-value
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
1-185 4.70e-65

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 198.26  E-value: 4.70e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   1 MIRLLPAGLYTEMPWKNGQGMTREVARYPEAGEY---DWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRS- 76
Cdd:COG3758    2 SMRILRAADLPRMPWKNGGGETREIARFPEGAGLddfDWRLSIATVAQDGPFSAFPGIDRTITLLEGDGLRLTVDGQGEh 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069  77 ALIAPFQALGFNGASGVSCEIVGGPLLDFNVIYREAALRATVSWC---GAGTWSHQGGLRILFNAGPALRVSVGDQRYLL 153
Cdd:COG3758   82 TLDEPFQPFAFSGDAPVSARLLGGPVRDFNLMTRRGRARARVRVLrlaGTLPLHADAGTGLLYVLAGAWTVALGGEAITL 161

                        170       180       190
                 ....*....|....*....|....*....|....
gi 503994069 154 EHYDSLLVDEAVAL--VIPDSPGARLARITLIPL 185
Cdd:COG3758  162 EAGDTLLLEAPAPLltLTPLSGDGRLLLVELTPR 195
HutD pfam05962
HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
 10-178 8.09e-43

HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilization operon. HutD is operonic with the well characterized repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. Evidence outlined by Zhang _ Rainey (2007) suggests that HutD functions as a governor that sets an upper bound on the level of hut operon transcription. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of PA5104 (HutD from Pseudomonas aeruginosa) show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.


Pssm-ID: 428694 [Multi-domain]  Cd Length: 180  Bit Score: 140.92  E-value: 8.09e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   10 YTEMPWKNGQGMTREVARYPEAGEYD---WRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGqRSALIAPFQALG 86
Cdd:pfam05962   4 YRRMPWKNGGGVTREIAIHPEGAGLDdfdWRLSIATVAQDGPFSAFPGIDRTLSLLEGDGMRLSVDG-PSRLLAPYQPFA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   87 FNGASGVSCEIVGGPLLDFNVIYREAALRATVSW----CGAGTWSHQGGLRILFNAGPALRVSVGDQ-RYLLEHYDSLLV 161
Cdd:pfam05962  83 FSGDAPVSARLLGGPIRDFNLMTRRGRATARVERlplvGGLTLAADGASTLLLYCLKGQVSVALDGGgTHTLAAGDCLLL 162

                         170
                  ....*....|....*..
gi 503994069  162 DEAVALVIPDSPGARLA 178
Cdd:pfam05962 163 EGPAALRLTLDGKGALL 179
cupin_HutD_N cd20293
histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model ...
 20-109 1.11e-38

histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380427  Cd Length: 92  Bit Score: 127.59  E-value: 1.11e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069  20 GMTREVARYPEAG--EYDWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRSALIAPFQALGFNGASGVSCEI 97
Cdd:cd20293    1 GTTREIARSPGGAgdDFDWRLSIADVAQDGPFSAFPGIDRILTVLEGAGMVLTVDGGEQVLLRPLQPFAFSGDAAVSARL 80

                         90
                 ....*....|..
gi 503994069  98 VGGPLLDFNVIY 109
Cdd:cd20293   81 LDGPVRDFNLMT 92
PRK11396 PRK11396
environmental stress-induced protein Ves;
2-118 1.48e-17

environmental stress-induced protein Ves;


Pssm-ID: 236905 [Multi-domain]  Cd Length: 191  Bit Score: 76.43  E-value: 1.48e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   2 IRLLPAGLytempWKNGQGMTREVARYPEAG-EYDWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRSALIA 80
Cdd:PRK11396   6 MRKMSVNL-----WRNAAGETREICTFPPAKrDFYWRASIASIAANGEFSLFPGMERIVTLLEGGEMFLESADRFNHTLK 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 503994069  81 PFQALGFNGASGVSCEIVGGPL-LDFNVIYREAALRATV 118
Cdd:PRK11396  81 PLQPFAFAADQVVKAKLTAGQMsMDFNIMTRLDVCKAKV 119
 
Name Accession Description Interval E-value
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
1-185 4.70e-65

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 198.26  E-value: 4.70e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   1 MIRLLPAGLYTEMPWKNGQGMTREVARYPEAGEY---DWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRS- 76
Cdd:COG3758    2 SMRILRAADLPRMPWKNGGGETREIARFPEGAGLddfDWRLSIATVAQDGPFSAFPGIDRTITLLEGDGLRLTVDGQGEh 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069  77 ALIAPFQALGFNGASGVSCEIVGGPLLDFNVIYREAALRATVSWC---GAGTWSHQGGLRILFNAGPALRVSVGDQRYLL 153
Cdd:COG3758   82 TLDEPFQPFAFSGDAPVSARLLGGPVRDFNLMTRRGRARARVRVLrlaGTLPLHADAGTGLLYVLAGAWTVALGGEAITL 161

                        170       180       190
                 ....*....|....*....|....*....|....
gi 503994069 154 EHYDSLLVDEAVAL--VIPDSPGARLARITLIPL 185
Cdd:COG3758  162 EAGDTLLLEAPAPLltLTPLSGDGRLLLVELTPR 195
HutD pfam05962
HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
 10-178 8.09e-43

HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilization operon. HutD is operonic with the well characterized repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. Evidence outlined by Zhang _ Rainey (2007) suggests that HutD functions as a governor that sets an upper bound on the level of hut operon transcription. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of PA5104 (HutD from Pseudomonas aeruginosa) show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.


Pssm-ID: 428694 [Multi-domain]  Cd Length: 180  Bit Score: 140.92  E-value: 8.09e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   10 YTEMPWKNGQGMTREVARYPEAGEYD---WRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGqRSALIAPFQALG 86
Cdd:pfam05962   4 YRRMPWKNGGGVTREIAIHPEGAGLDdfdWRLSIATVAQDGPFSAFPGIDRTLSLLEGDGMRLSVDG-PSRLLAPYQPFA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   87 FNGASGVSCEIVGGPLLDFNVIYREAALRATVSW----CGAGTWSHQGGLRILFNAGPALRVSVGDQ-RYLLEHYDSLLV 161
Cdd:pfam05962  83 FSGDAPVSARLLGGPIRDFNLMTRRGRATARVERlplvGGLTLAADGASTLLLYCLKGQVSVALDGGgTHTLAAGDCLLL 162

                         170
                  ....*....|....*..
gi 503994069  162 DEAVALVIPDSPGARLA 178
Cdd:pfam05962 163 EGPAALRLTLDGKGALL 179
cupin_HutD_N cd20293
histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model ...
 20-109 1.11e-38

histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model represents the N-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380427  Cd Length: 92  Bit Score: 127.59  E-value: 1.11e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069  20 GMTREVARYPEAG--EYDWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRSALIAPFQALGFNGASGVSCEI 97
Cdd:cd20293    1 GTTREIARSPGGAgdDFDWRLSIADVAQDGPFSAFPGIDRILTVLEGAGMVLTVDGGEQVLLRPLQPFAFSGDAAVSARL 80

                         90
                 ....*....|..
gi 503994069  98 VGGPLLDFNVIY 109
Cdd:cd20293   81 LDGPVRDFNLMT 92
PRK11396 PRK11396
environmental stress-induced protein Ves;
2-118 1.48e-17

environmental stress-induced protein Ves;


Pssm-ID: 236905 [Multi-domain]  Cd Length: 191  Bit Score: 76.43  E-value: 1.48e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994069   2 IRLLPAGLytempWKNGQGMTREVARYPEAG-EYDWRISLATIRQPGPFSAFPGYLRNISVLEGGGMYLTIDGQRSALIA 80
Cdd:PRK11396   6 MRKMSVNL-----WRNAAGETREICTFPPAKrDFYWRASIASIAANGEFSLFPGMERIVTLLEGGEMFLESADRFNHTLK 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 503994069  81 PFQALGFNGASGVSCEIVGGPL-LDFNVIYREAALRATV 118
Cdd:PRK11396  81 PLQPFAFAADQVVKAKLTAGQMsMDFNIMTRLDVCKAKV 119
cupin_HutD_C cd20490
histidine utilization protein HutD and related proteins, C-terminal cupin domain; This model ...
 135-185 4.79e-03

histidine utilization protein HutD and related proteins, C-terminal cupin domain; This model represents the C-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380447  Cd Length: 77  Bit Score: 34.51  E-value: 4.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503994069 135 LFNAGPALRVSV-GDQRYLLEHYDSLLVDEAVALVIPDSPGARLARITLIPL 185
Cdd:cd20490   25 LFSAGEGLAVSLdGHAAQQLGRHDCLQLEGNAGLAELRLSGAGAGRCCLIEL 76
 
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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