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33  structures 1716  species 0  interactions 2710  sequences 6  architectures

Family: Toluene_X (PF03349)

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...

FadL outer membrane protein transport family Edit Wikipedia article

Outer membrane transport proteins (OMPP1/FadL/TodX)
1t16 opm.gif
Structure of the bacterial fatty acid transporter FadL.[1]
Identifiers
Symbol Toluene_X
Pfam PF03349
Pfam clan CL0193
InterPro IPR005017
TCDB 1.B.9
OPM superfamily 30
OPM protein 1t16

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.

Notes[edit]

  1. ^ Van Den Berg, B.; Black, P. N.; Clemons Jr, W. M.; Rapoport, T. A. (2004). "Crystal Structure of the Long-Chain Fatty Acid Transporter FadL". Science 304 (5676): 1506–1509. doi:10.1126/science.1097524. PMID 15178802. 

References[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Literature references

  1. 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

  2. Kahng HY, Byrne AM, Olsen RH, Kukor JJ; , J Bacteriol 2000;182:1232-1242.: Characterization and role of tbuX in utilization of toluene by Ralstonia pickettii PKO1. PUBMED:10671442 EPMC:10671442

  3. 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

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 and TbuX from Burkholderia pickettii (Ralstonia pickettii) (Pseudomonas pickettii) PKO1 SWISSPROT. 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.

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 MBB (CL0193), which has the following description:

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 54 members:

Ail_Lom Autotransporter Bac_surface_Ag Campylo_MOMP Channel_Tsx CopB DUF1302 DUF1597 DUF2320 DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3374 DUF3575 DUF4289 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL Phenol_MetA_deg Porin_1 Porin_2 Porin_4 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(22)
Full
(2710)
Representative proteomes NCBI
(2172)
Meta
(277)
RP15
(153)
RP35
(342)
RP55
(479)
RP75
(577)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(22)
Full
(2710)
Representative proteomes NCBI
(2172)
Meta
(277)
RP15
(153)
RP35
(342)
RP55
(479)
RP75
(577)
Alignment:
Format:
Order:
Sequence:
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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
(22)
Full
(2710)
Representative proteomes NCBI
(2172)
Meta
(277)
RP15
(153)
RP35
(342)
RP55
(479)
RP75
(577)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: Pfam-B_3708 (release 6.5)
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 22
Number in full: 2710
Average length of the domain: 395.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 92.57 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 427
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Structures

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 33 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 seqence.

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