Summary: PAS domain
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PAS domain Edit Wikipedia article
The PAS domain is a protein domain contained in many signaling proteins where it functions as a signal sensor. PAS domains are found in a large number of organisms from bacteria to humans. The PAS domain was named after the three proteins in which it was first discovered:
- Per – period circadian protein
- Arnt – aryl hydrocarbon receptor nuclear translocator protein
- Sim – single-minded protein
- PDB 1y28; Dunham CM, Dioum EM, Tuckerman JR, Gonzalez G, Scott WG, Gilles-Gonzalez MA (July 2003). "A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure". Biochemistry 42 (25): 7701–8. doi:10.1021/bi0343370. PMID 12820879.
- Ponting CP, Aravind L (November 1997). "PAS: a multi-functional domain family comes to light". Curr. Biol. 7 (11): R674–7. doi:10.1016/S0960-9822(06)00352-6. PMID 9382818.
- Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J (March 2004). "The PAS fold. A redefinition of the PAS domain based upon structural prediction". Eur. J. Biochem. 271 (6): 1198–208. doi:10.1111/j.1432-1033.2004.04023.x. PMID 15009198.
- Gilles-Gonzalez MA, Gonzalez G (February 2004). "Signal transduction by heme-containing PAS-domain proteins". J. Appl. Physiol. 96 (2): 774–83. doi:10.1152/japplphysiol.00941.2003. PMID 14715687.
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|Similarity to PfamA using HHSearch:||PAS PAS_2 PAS_3 PAS_4 MEKHLA PAS_7 PAS_8 PAS_10 PAS_11|
External database links
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- the number of sequences which exhibit this architecture
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This clan contains PAS domains that are found in a wide variety of bacterial signaling proteins.
The clan contains the following 13 members:MEKHLA PAS PAS_10 PAS_11 PAS_2 PAS_3 PAS_4 PAS_5 PAS_6 PAS_7 PAS_8 PAS_9 PocR
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
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Curation and family details
|Number in seed:||245|
|Number in full:||26423|
|Average length of the domain:||103.90 aa|
|Average identity of full alignment:||18 %|
|Average coverage of the sequence by the domain:||17.69 %|
|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:||1|
|Download:||download the raw HMM for this family|
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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 PAS_9 domain has been found. There are 105 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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