Summary: Outer membrane protein transport protein (OMPP1/FadL/TodX)
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This is the Wikipedia entry entitled "FadL outer membrane protein transport family". More...
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FadL outer membrane protein transport family Edit Wikipedia article
|Outer membrane transport proteins (OMPP1/FadL/TodX)|
Outer membrane transport proteins (OMPP1/FadL/TodX) family includes several proteins that are involved in toluene catabolism and degradation of aromatic hydrocarbons. This family also includes protein FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2.
- Wang Y, Rawlings M, Gibson DT, LabbÃ© D, Bergeron H, Brousseau R, Lau PC (March 1995). "Identification of a membrane protein and a truncated LysR-type regulator associated with the toluene degradation pathway in Pseudomonas putida F1". Molecular & General Genetics. 246 (5): 570â€“9. doi:10.1007/bf00298963. PMIDÂ 7535376. S2CIDÂ 13211193.
- Kahng HY, Byrne AM, Olsen RH, Kukor JJ (March 2000). "Characterization and role of tbuX in utilization of toluene by Ralstonia pickettii PKO1". Journal of Bacteriology. 182 (5): 1232â€“42. doi:10.1128/jb.182.5.1232-1242.2000. PMCÂ 94407. PMIDÂ 10671442.
- Eaton RW (May 1997). "p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate". Journal of Bacteriology. 179 (10): 3171â€“80. doi:10.1128/jb.179.10.3171-3180.1997. PMCÂ 179094. PMIDÂ 9150211.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Outer membrane protein transport protein (OMPP1/FadL/TodX) Provide feedback
This family includes TodX from Pseudomonas putida F1 Q51971 and TbuX from Ralstonia pickettii PKO1 Q9RBW8. These are membrane proteins of uncertain function that are involved in toluene catabolism. Related proteins involved in the degradation of similar aromatic hydrocarbons are also in this family, such as CymD O33458. This family also includes FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2.
Wang Y, Rawlings M, Gibson DT, Labbe D, Bergeron H, Brousseau R, Lau PC; , Mol Gen Genet 1995;246:570-579.: Identification of a membrane protein and a truncated LysR-type regulator associated with the toluene degradation pathway in Pseudomonas putida F1. PUBMED:7535376 EPMC:7535376
Eaton RW; , J Bacteriol 1997;179:3171-3180.: p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. PUBMED:9150211 EPMC:9150211
Internal database links
|SCOOP:||Autotransporter BBP2 DUF2490 MtrB_PioB OMP_b-brl OmpA_membrane Porin_2 Porin_4 PorV TonB_dep_Rec|
|Similarity to PfamA using HHSearch:||DUF2490|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005017
This family includes TodX from Pseudomonas putida (strain F1/ATCC 700007) SWISSPROT [ PUBMED:7535376 , PUBMED:9150211 ] and TbuX from Burkholderia pickettii (Ralstonia pickettii) (Pseudomonas pickettii) PKO1 SWISSPROT [ PUBMED:10671442 ]. These are membrane proteins of uncertain function that are involved in toluene catabolism. Related proteins involved in the degradation of similar aromatic hydrocarbons are also in this family, such as CymD SWISSPROT . This family also includes FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 117 members:Ail_Lom Alginate_exp Attacin_C Attacin_N Autotransporter BBP2 BBP2_2 BBP7 BCSC_C Campylo_MOMP Caps_assemb_Wzi CBP_BcsS Channel_Tsx Chlam_OMP CopB CymA DcaP DUF1207 DUF1302 DUF1842 DUF2219 DUF2490 DUF2715 DUF2860 DUF3034 DUF3078 DUF3138 DUF3187 DUF3373 DUF3570 DUF3573 DUF3575 DUF3769 DUF3996 DUF4421 DUF4595 DUF481 DUF4840 DUF5020 DUF5686 DUF5723 DUF5777 DUF5916 DUF6048 DUF6089 DUF6268 Gcw_chp GrlR HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C LptD LptD_2 MDM10 MipA MOSP_C MSP MtrB_PioB NfrA_C Omp85 Omp85_2 Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF PagL PagP Phenol_MetA_deg PLA1 Pom Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_5 Porin_6 Porin_7 Porin_8 Porin_O_P Porin_OmpG Porin_OmpG_1_2 Porin_OmpL1 PorP_SprF PorV Serpulina_VSP ShlB SlipAM Surface_Ag_2 TbpB_B_D Toluene_X TonB_dep_Rec TraF_2 TraO TSA UPF0164 UPF0257 Usher Usher_TcfC YadA_anchor YaiO YfaZ YjbH
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There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
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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.
|Seed source:||Pfam-B_3708 (release 6.5)|
|Number in seed:||10|
|Number in full:||3897|
|Average length of the domain:||375.30 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||88.38 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
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If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 Toluene_X domain has been found. There are 36 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.
Loading structure mapping...
AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
|Protein||Predicted structure||External Information|
|P10384||View 3D Structure||Click here|
|P43838||View 3D Structure||Click here|
|P59741||View 3D Structure||Click here|
|P80603||View 3D Structure||Click here|
|Q8XCN6||View 3D Structure||Click here|
|Q8ZNA5||View 3D Structure||Click here|
|Q9K1M2||View 3D Structure||Click here|