Difference between revisions of "Phosphatase Subfamily FCP1 Tech Notes"
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====== Use ''C. elegans'' FCP1 CTD ====== | ====== Use ''C. elegans'' FCP1 CTD ====== | ||
| − | We then PSI-BLASTed the region right next to BRCT domain (432-659) of ''C. elegans'' FCP1. We | + | We then PSI-BLASTed the region right next to BRCT domain (432-659) of ''C. elegans'' FCP1. We found there is a mild conservation in Caenorhabditis. The best hits after those of Caenorhabditis are Human coronavirus polyprotein 1ab. We therefore conclude that C. elegans or Caenorhabditis in general lacks the FCP1 domain. The full sequence of ''C. elegans'' FCP1 is below: |
MDIKFEGNDAECTAGLKKASEGSFVLKDHVLIEFKINGKVAGKIKTPCEGVVTFGKGLKPGIVLNKGQVIATVSECTHAIVIKDMCATCGKDLREKGGRAGQRKEQSTANVSMIHHVPELIVSDTLAKEIGSADENNLITNRKLVLLVDLDQTIIHTSDKPMTVDTENHKDITKYNLHSRVYTTKLRPHTTEFLNKMSNMYEMHIVTYGQRQYAHRIAQILDPDARLFEQRILSRDELFSAQHKTNNLKALFPCGDNLVVIIDDRSDVWMYSEALIQIKPYRFFKEVGDINAPKNSKEQMPVQIEDDAHEDKVLEEIERVLTNIHDKYYEKHDLRGSEEVLLDVKEVIKEERHKVLDGCVIVFSGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDDVTHVVGARYGTQKVYQANRLNKFVVTVQWVYACVEKWLKADENLFQLTKESTPPVGRPLGSKYVNDLANMDTIGKAALADMNNEVDEALSDDEDDGDNEDEDDDGNDVGEDKGDENLEEKQEKNEEEMDDVEQNGSVENQSGDALENETDSTSRGQKRKHCPEMEDEEEESDSDNEDDDTPMSYKALLSDSRKKGRIVPENEDDAVFDVDDEKGHAPANIDEEEDDEDNEDEEVPESDDDDEFEDMAALIERQISDAVDEKDQ | MDIKFEGNDAECTAGLKKASEGSFVLKDHVLIEFKINGKVAGKIKTPCEGVVTFGKGLKPGIVLNKGQVIATVSECTHAIVIKDMCATCGKDLREKGGRAGQRKEQSTANVSMIHHVPELIVSDTLAKEIGSADENNLITNRKLVLLVDLDQTIIHTSDKPMTVDTENHKDITKYNLHSRVYTTKLRPHTTEFLNKMSNMYEMHIVTYGQRQYAHRIAQILDPDARLFEQRILSRDELFSAQHKTNNLKALFPCGDNLVVIIDDRSDVWMYSEALIQIKPYRFFKEVGDINAPKNSKEQMPVQIEDDAHEDKVLEEIERVLTNIHDKYYEKHDLRGSEEVLLDVKEVIKEERHKVLDGCVIVFSGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDDVTHVVGARYGTQKVYQANRLNKFVVTVQWVYACVEKWLKADENLFQLTKESTPPVGRPLGSKYVNDLANMDTIGKAALADMNNEVDEALSDDEDDGDNEDEDDDGNDVGEDKGDENLEEKQEKNEEEMDDVEQNGSVENQSGDALENETDSTSRGQKRKHCPEMEDEEEESDSDNEDDDTPMSYKALLSDSRKKGRIVPENEDDAVFDVDDEKGHAPANIDEEEDDEDNEDEEVPESDDDDEFEDMAALIERQISDAVDEKDQ | ||
Revision as of 20:51, 15 October 2015
Phosphatase Classification: Fold HAD: Superfamily HAD: Family FCP: Subfamily FCP1: Technical Notes
Contents
FCP1_C domain
Using Pfam profile
In order to find FCP1_C domain phylogenetic distribution among FCP1, we obtained the FCP1 from our internal orthology database, which contains 227 from 183 eukaryotic genomes. We then searched the FCP1_C domain by Pfam web server.
We also searched the FCP1_C domain region of human FCP1 defined by Pfam against NR dataset limiting to metazoa excluding deuterosomes through NCBI BLAST server. We found no hit has E-value lower than 0.1. We did not find FCP1_C in nematostella sequence in NR dataset, because our updated nematostella sequence is different from the one in NR.
PSI-BLAST
Use human FCP1 CTD
We first PSI-BLASTed the FCP1_C region (716-961 as defined by CDD) of human FCP1. We eyeballed the hits in the third round, which started to contain animal KIAA0556, but failed to hit any region in Drosophila melanogaster FCP1. We then stopped our search using human FCP1. The full sequence of human FCP1 is below:
MEVPAAGRVPAEGAPTAAVAEVRCPGPAPLRLLEWRVAAGAAVRIGSVLAVFEAAASAQSSGASQSRVASGGCVRPARPERRLRSERAGVVRELCAQPGQVVAPGAVLVRLEGCSHPVVMKGLCAECGQDLTQLQSKNGKQQVPLSTATVSMVHSVPELMVSSEQAEQLGREDQQRLHRNRKLVLMVDLDQTLIHTTEQHCQQMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTGNLRNLFPCGDSMVCIIDDREDVWKFAPNLITVKKYVYFQGTGDMNAPPGSRESQTRKKVNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPEGAGALAQGSSLEPGRPAAPSLPGEAEPGAHAPDKEPELGGQEEGERDGLCGLGNGCADRKEAETESQNSELSGVTAGESLDQSMEEEEEEDTDEDDHLIYLEEILVRVHTDYYAKYDRYLNKEIEEAPDIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHATALGAKILTRLVLSPDAPDRATHLIAARAGTEKVLQAQECGHLHVVNPDWLWSCLERWDKVEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGKLIRTGARGPPAPSSSLPIRQEPSSFRAVPPPQPQMFGEELPDAQDGEQPGPSRRKRQPSMSETMPLYTLCKEDLESMDKEVDDILGEGSDDSDSEKRRPEEQEEEPQPRKPGTRRERTLGAPASSERSAAGGRGPRGHKRKLNEEDAASESSRESSNEDEGSSSEADEMAKALEAELNDLM
Use fruit fly FCP1 CTD
We then PSI-BLASTed the region right next to BRCT domain (668-880) of fruit fly FCP1. We eyeballed the hits in each round. We found the 4th round hit most FCP1 better the threshold (E-value 0.005) and most of the hits worse the threshold are genes of other families. We then downloaded the sequences and built HMM. The profile built can detect CTD in nematostella, fruit fly, sea urchin, and human among the nine genomes. The full sequence of fruit fly FCP1 is below:
MQNIPDEEGATPSRAPGGVAASGAAEGDDGGGGSGAKNSASGNSNNNTSGGGIIVLRAALGENEARAVINKWRVREGQFVSAAQILFLYQPVGVDAKDAKDAGKPGGDCAIQRYKSQRAGVVKKRLRKEGELLTKGDAILELSECIHTTVIKDMCADCGADLRQNENGQTSEASVPMVHTMPDLKVTQKLAQKLGHDDTRRLLADRKLVLLVDLDQTVIHTTNDTVPDNIKGIYHFQLYGPHSPWYHTRLRPGTAEFLERMSQLYELHICTFGARNYAHMIAQLLDPEGKFFSHRILSRDECFNATSKTDNLKALFPNGDSMVCIIDDREDVWNMASNLIQVKPYHFFQHTGDINAPPGLSKHELDGEGVDFKEITEKHGDKDKTESSSEVKPEDTDKGDNTVTSTSKDDDVNEESVDVFEIEGDAKDPEVSNASSATEAPKEPRDKLNGKTNAEDIVVIDDSSSGSPDAEKAASDGEDVVVIDDNSKESTKAEVPPTPAEKNEVVASSTTSPDEKRPSADADVATTSKTPSLRAPLEGQKQIEIEDPDDYLLYLEVILRNIHKRFYSIYDETTEIPDLKVIVPKIRSEVLRGKNLVFSGLVPTQMKLEQSRAYFIAKSLGAEVKPNIDKEITHLVAVNAGTYKVNAAKKEPAIKVVNANWLWTCAERWEHVEEKLFPLDRKVRNKGRQPPAHCHSPEHVVNYSERSEISPSSSKQQEEQSGNFRETLNPLLVFTNADIESMNKDYETFFESDSSSDEGPVNFENPPMDKKLLKRKREDDNSNRAHDFFTRSDDIMIGAPNLVEVDISSNEEADDNNEKEDDDDEMPSAKFRRGEDLPSDLELGSESNSEKEPEDEDDGEWNMMGAALEREFLGLEDFDM
Use C. elegans FCP1 CTD
We then PSI-BLASTed the region right next to BRCT domain (432-659) of C. elegans FCP1. We found there is a mild conservation in Caenorhabditis. The best hits after those of Caenorhabditis are Human coronavirus polyprotein 1ab. We therefore conclude that C. elegans or Caenorhabditis in general lacks the FCP1 domain. The full sequence of C. elegans FCP1 is below:
MDIKFEGNDAECTAGLKKASEGSFVLKDHVLIEFKINGKVAGKIKTPCEGVVTFGKGLKPGIVLNKGQVIATVSECTHAIVIKDMCATCGKDLREKGGRAGQRKEQSTANVSMIHHVPELIVSDTLAKEIGSADENNLITNRKLVLLVDLDQTIIHTSDKPMTVDTENHKDITKYNLHSRVYTTKLRPHTTEFLNKMSNMYEMHIVTYGQRQYAHRIAQILDPDARLFEQRILSRDELFSAQHKTNNLKALFPCGDNLVVIIDDRSDVWMYSEALIQIKPYRFFKEVGDINAPKNSKEQMPVQIEDDAHEDKVLEEIERVLTNIHDKYYEKHDLRGSEEVLLDVKEVIKEERHKVLDGCVIVFSGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDDVTHVVGARYGTQKVYQANRLNKFVVTVQWVYACVEKWLKADENLFQLTKESTPPVGRPLGSKYVNDLANMDTIGKAALADMNNEVDEALSDDEDDGDNEDEDDDGNDVGEDKGDENLEEKQEKNEEEMDDVEQNGSVENQSGDALENETDSTSRGQKRKHCPEMEDEEEESDSDNEDDDTPMSYKALLSDSRKKGRIVPENEDDAVFDVDDEKGHAPANIDEEEDDEDNEDEEVPESDDDDEFEDMAALIERQISDAVDEKDQ
