IGEM:UNAM-Genomics Mexico/2009/Notebook/H2/2011/03/24

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Operon?

 * It would appear that in Shewanella, our genes do form an operon (HydA, HydB, fdh, HydG, HydX, HydE, & HydF).
 * Source doi:10.1128/AEM.01588-06
 * However, in our Chlamydomonas reinhardtti they form no such operon.
 * HydAa
 * HydA2
 * HydEF
 * HydG
 * The only ones close to each other are HydEF & HydG, but they are on opposite strands. Therefore, in the search for Chaperone X, I'll search Chlamydomonas por HydX, & HydB, as fdh is some sort of electron-donnor (formate dehydrogenase).


 * For HydX, it encodes a hypothetical 213aa protein of accesion code AAN56899
 * Source doi:10.1371/journal.pone.0015491
 * However, a BLASTp search returned a bunch of strong hypothetical proteins, and a greater bunch of highly diverse ones. Narrowing the search to taxon:Chlamydomonas reinhardtti, the searched returned just a few unrelated and hypothetical proteins. Therefore, it is highly dubious this HydX is present in the C.reinhardtti genome, therefore we would not requrie it to assure correct Tat export.


 * For HydB, it encodes a 106aa protein of accesion code AE014299.1 or NP_719452 (both yield exact same AA sequence)
 * Source NCBI search.
 * A BLATp search returned a great diversity of hits, all conserned with FeFe hydrogenases. It appears it is the latter half of the protein that is conserved. Repeating the search with taxon as Chlamydomonas reinhardtti restriction returned the HydA2 small subunit of the HydA1-HydA2 chloroplast hydrogenase. This is obviously not responsible for localization to the periplasm.


 * As a general conclusion, there appears to be no chaperone involved in HydA1 maturation or delay for translocation by the Tat system in Chlamydomonas reinhardtti. Thus, if we use said hydrogenase, we should not have issues with it's export (unless the maturases HydEFG from Shewanella oneidensis mess with us...).

PFOR

 * From Silver's Paper, to the reference, to the NCBI entry. The sequence is:
 * Source

1 mgkkmmttdg ntatahvaya msevaaiypi tpsstmgeea ddwaaqgrkn ifgqtltire 61 mqseagaaga vhgalaagal tttftasqgl llmipnmyki sgellpgvfh vtaraiaaha 121 lsifgdhqdi yaarqtgfam lasssvqeah dmalvahlaa iesnvpfmhf fdgfrtshei 181 qkievldyad maslvnqkal aefraksmnp ehphvrgtaq npdiyfqgre aanpyylkvp 241 givaeymqkv asltgrsykl fdyvgapdae rvivsmgssc etieevinhl aakgekigli 301 kvrlyrpfvs eaffaalpas akvitvldrt kepgapgdpl yldvcsafve rgeampkila 361 gryglgskef spamvksvyd nmsgakknhf tvgieddvtg tslpvdnafa dttpkgtiqc 421 qfwglgadgt vgankqaiki igdntdlfaq gyfsydskks ggitishlrf gekpiqstyl 481 vnradyvach npayvgiydi legikdggtf vlnspwssle dmdkhlpsgi krtiankklk 541 fynidavkia tdvglggrin mimqtaffkl agvlpfekav dllkksihka ygkkgekivk 601 mntdavdqav tslqefkypd swkdapaetk aepmtneffk nvvkpiltqq gdklpvsafe 661 adgrfplgts qfekrgvain vpqwvpenci qcnqcafvcp hsailpvlak eeelvgapan 721 ftaleakgke lkgykfriqi ntldcmgcgn cadicppkek alvmqpldtq rdaqvpnley 781 aaripvksev lprdslkgsq fqeplmefsg acsgcgetpy vrvitqlfge rmfianatgc 841 ssiwgasaps mpyktnrlgq gpawgnslfe daaeygfgmn msmfarrthl adlaakales 901 dasgdvkeal qgwlagkndp ikskeygdkl kkllagqkdg llgqiaamsd lytkksvwif 961 ggdgwaydig yggldhvlas gedvnvfvmd tevysntggq sskatptgav akfaaagkrt 1021 gkkdlarmvm tygyvyvatv smgyskqqfl kvlkeaesfp gpslviayat cinqglrkgm 1081 gksqdvmnta vksgywplfr ydprlaaqgk npfqldskap dgsveeflma qnrfavldrs 1141 fpedakrlra qvaheldvrf kelehmaatn ifesfapagg kadgsvdfge gaefctrddt 1201 pmmarpdsge acdqnragts eqqgdlskrt kk


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