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161  structures 618  species 1  interaction 3174  sequences 10  architectures

Family: Bac_rhodopsin (PF01036)

Summary: Bacteriorhodopsin-like protein

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This is the Wikipedia entry entitled "Bacterial rhodopsins". More...

Bacterial rhodopsins Edit Wikipedia article

Bacteriorhodopsin-like protein
1m0l opm.gif
Bacteriorhodopsin trimer
Identifiers
Symbol Bac_rhodopsin
Pfam PF01036
InterPro IPR001425
PROSITE PDOC00291
SCOP 2brd
SUPERFAMILY 2brd
TCDB 3.E.1
OPM family 6
OPM protein 1vgo

Bacterial rhodopsins are a family of bacterial opsins. They are retinal-binding proteins that provide light-dependent ion transport and sensory functions to a family of halophilic[1][2] and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point for retinal (a conserved lysine).

The proteins from halobacteria include bacteriorhodopsin and archaerhodopsin, which are light-driven proton pumps; halorhodopsin, a light-driven chloride pump; and sensory rhodopsin, which mediates both photoattractant (in the red) and photophobic (in the ultra-violet) responses. Proteins from other bacteria include proteorhodopsin.

[edit] References

  1. ^ Oesterhelt D, Tittor J (1989). "Two pumps, one principle: light-driven ion transport in halobacteria". Trends Biochem. Sci. 14 (2): 57–61. doi:10.1016/0968-0004(89)90044-3. PMID 2468194. 
  2. ^ Lottspeich F, Oesterhelt D, Blanck A, Ferrando E, Schegk ES (1989). "Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor". EMBO J. 8 (13): 3963–3971. PMC 401571. PMID 2591367. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=401571. 


This article incorporates text from the public domain Pfam and InterPro IPR001425

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.

Bacteriorhodopsin-like protein Provide feedback

The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: O74870 P25619 P38079 Q12117.

Literature references

  1. Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R; , J Mol Biol 1996;259:393-421.: Electron-crystallographic refinement of the structure of bacteriorhodopsin. PUBMED:8676377 EPMC:8676377

  2. Oesterhelt D, Tittor J;, Trends Biochem Sci. 1989;14:57-61.: Two pumps, one principle: light-driven ion transport in halobacteria. PUBMED:2468194 EPMC:2468194

  3. Blanck A, Oesterhelt D, Ferrando E, Schegk ES, Lottspeich F;, EMBO J. 1989;8:3963-3971.: Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor. PUBMED:2591367 EPMC:2591367


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001425

Bacterial rhodopsins are a family of bacterial opsins. They are retinal-binding proteins that provide light-dependent ion transport and sensory functions to a family of halophilic bacteria [PUBMED:2468194, PUBMED:2591367]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal binding (a conserved lysine).

The archaeal/bacterial/fungal rhodopsin family includes bacteriorhodopsin and archaerhodopsin, which are light-driven proton pumps; halorhodopsin, a light-driven chloride pump; and sensory rhodopsin, which mediates both photoattractant (in the red) and photophobic (in the UV) responses. This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: SWISSPROT, SWISSPROT, SWISSPROT, SWISSPROT.

Gene Ontology

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Domain organisation

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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
(17)
Full
(3174)
Representative proteomes NCBI
(3093)
Meta
(2566)
RP15
(69)
RP35
(151)
RP55
(216)
RP75
(242)
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Format an alignment

  Seed
(17)
Full
(3174)
Representative proteomes NCBI
(3093)
Meta
(2566)
RP15
(69)
RP35
(151)
RP55
(216)
RP75
(242)
Alignment:
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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
(17)
Full
(3174)
Representative proteomes NCBI
(3093)
Meta
(2566)
RP15
(69)
RP35
(151)
RP55
(216)
RP75
(242)
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.

Pfam alignments:

HMM logo

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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_1412 (release 3.0)
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 17
Number in full: 3174
Average length of the domain: 141.90 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 89.93 %

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 21.9 21.9
Trusted cut-off 21.9 21.9
Noise cut-off 21.3 21.8
Model length: 222
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Bac_rhodopsin

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 Bac_rhodopsin domain has been found. There are 161 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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