HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
1-181
1.45e-127
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.
The actual alignment was detected with superfamily member PRK11396:
Pssm-ID: 445457 [Multi-domain] Cd Length: 191 Bit Score: 356.09 E-value: 1.45e-127
HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
5-175
8.55e-49
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: 156.32 E-value: 8.55e-49
histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model ...
19-109
1.51e-31
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: 109.10 E-value: 1.51e-31
HutD; HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and ...
5-175
8.55e-49
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: 156.32 E-value: 8.55e-49
histidine utilization protein HutD and related proteins, N-terminal cupin domain; This model ...
19-109
1.51e-31
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: 109.10 E-value: 1.51e-31
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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(labeled illustration) Four types of hits can be shown, as available,
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specific hits meet or exceed a domain-specific e-value threshold
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
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Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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