Summary: HutD
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HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilisation operon. HutD is operonic with the well characterised 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 [1]. 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.
Literature references
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Zhang XX, Rainey PB; , Genetics. 2007;176:2165-2176.: Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. PUBMED:17717196 EPMC:17717196
This tab holds annotation information from the InterPro database.
InterPro entry IPR010282
This entry contains proteins of unknown function, which include HutD from Pseudomonas fluorescens and Ves from Escherichia coli K12.
HutD from P. fluorescens is a component of the histidine uptake and utilisation operon. HutD is operonic with the well characterised 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. HutD probably sets an upper bound on the level of hut operon transcription [PUBMED:17717196]. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of HutD from Pseudomonas aeruginosa show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Cupin (CL0029), which has the following description:
This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.
The clan contains the following 65 members:
2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AIM24 AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox AUDH_Cupin Auxin_BP CDO_I CENP-C_C cNMP_binding CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DIOX_N DMSP_lyase dTDP_sugar_isom DUF1479 DUF1971 DUF386 DUF4437 DUF4867 DUF5070 Ectoine_synth ERG2_Sigma1R EutQ FdtA FTO_NTD GPI HgmA HutD JmjC JmjN KduI Lyx_isomer MannoseP_isomer Ofd1_CTDD Oxygenase-NA PCO_ADO PhyH Pirin Pirin_C Pirin_C_2 PMI_typeI Popeye Pox_C4_C10 Ppnp TauD Tet_JBP Ureidogly_lyase VIT VIT_2Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (57) |
Full (1351) |
Representative proteomes | UniProt (4929) |
NCBI (8441) |
Meta (43) |
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RP15 (187) |
RP35 (716) |
RP55 (1344) |
RP75 (2413) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (57) |
Full (1351) |
Representative proteomes | UniProt (4929) |
NCBI (8441) |
Meta (43) |
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RP15 (187) |
RP35 (716) |
RP55 (1344) |
RP75 (2413) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_5160 (release 9.0) |
Previous IDs: | DUF886; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Moxon SJ |
Number in seed: | 57 |
Number in full: | 1351 |
Average length of the domain: | 173.20 aa |
Average identity of full alignment: | 26 % |
Average coverage of the sequence by the domain: | 85.13 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 183 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
HutDStructures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HutD domain has been found. There are 8 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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