Summary: Ethanolamine utilisation - propanediol utilisation
Ethanolamine utilisation - propanediol utilisation Provide feedback
Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood [1-3].
Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth JR; , J Bacteriol. 2004;186:7635-7644.: Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica. PUBMED:15516577 EPMC:15516577
Kofoid E, Rappleye C, Stojiljkovic I, Roth J; , J Bacteriol 1999;181:5317-5329.: The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. PUBMED:10464203 EPMC:10464203
Bobik TA, Havemann GD, Busch RJ, Williams DS, Aldrich HC; , J Bacteriol. 1999;181:5967-5975.: The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B(12)-dependent 1, 2-propanediol degradation. PUBMED:10498708 EPMC:10498708
Internal database links
|Similarity to PfamA using HHSearch:||AAA ATP_bind_1 GTP_EFTU ABC_tran AIG1 Arf DUF258 Dynamin_N FeoB_N Septin Gtr1_RagA Mg_chelatase MMR_HSR1 MobB Ras RNA_helicase NACHT AAA_5 Miro SRPRB AAA_10 AAA_16 AAA_17 AAA_18 AAA_21 AAA_22 AAA_23 AAA_28 AAA_29 AAA_33|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR012381
Members of this family function in ethanolamine [PUBMED:10464203] and propanediol [PUBMED:10498708] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively.
The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems.
Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [PUBMED:10498708, PUBMED:9023178]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [PUBMED:9539791, PUBMED:9922242]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [PUBMED:1312999, PUBMED:8226666, PUBMED:1313000]. Please see INTERPRO, INTERPRO, INTERPRO, INTERPRO, INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||ATP binding (GO:0005524)|
|Biological process||cellular biogenic amine metabolic process (GO:0006576)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||FIG047026 (Release 2.0)|
|Author:||FIGfam, Mistry J, Coggill P|
|Number in seed:||20|
|Number in full:||1157|
|Average length of the domain:||127.50 aa|
|Average identity of full alignment:||43 %|
|Average coverage of the sequence by the domain:||87.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||4|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree