Phosphatase Subfamily FCP1 Tech Notes - Revision history

Mark: /* Use Dicty FCP1 CTD */

2015-10-15T21:23:49Z

‎Use Dicty FCP1 CTD

Mark at 21:21, 15 October 2015

2015-10-15T21:21:12Z

Mark at 21:17, 15 October 2015

2015-10-15T21:17:53Z

Mark: /* Use fruit fly FCP1 CTD */

2015-10-15T21:00:28Z

‎Use fruit fly FCP1 CTD

Mark: /* Use C. elegans FCP1 CTD */

2015-10-15T20:59:51Z

‎Use C. elegans FCP1 CTD

Mark: /* Use fruit fly FCP1 CTD */

2015-10-15T20:59:17Z

‎Use fruit fly FCP1 CTD

Mark: /* Use C. elegans FCP1 CTD */

2015-10-15T20:51:21Z

‎Use C. elegans FCP1 CTD

Mark at 20:46, 15 October 2015

2015-10-15T20:46:35Z

Mark: /* PSI-BLAST */

2015-10-15T19:01:56Z

‎PSI-BLAST

Mark: /* PSI-BLAST */

2015-10-15T19:01:46Z

‎PSI-BLAST

@@ Line 27: / Line 27: @@
 We PSI-BLASTed the region right next to BRCT domain of budding yeast FCP1. We found hits in some but not all Saccharomycetales. Meanwhile, the sequences are not very similar to each other. We therefore conclude that budding yeast lacks the FCP1 CTD domain.
-====== Use Dicty FCP1 CTD ======
+====== Use Dicty, sponge, Monosiga, FCP1 CTD ======
 Dicty has two FCP1s. One has BRCT right at the C-terminal, which means it lacks FCP1 CTD domain. We PSI-BLASTed the region right next to BRCT domain, but there is only one hit except itself, which is a gene of D. purpureum, and the sequence similarity is weak, even cannot make a global alignment. We therefore conclude that Dicty lacks the FCP1 CTD domain.

← Older revision		Revision as of 21:21, 15 October 2015
Line 25:		Line 25:

	====== Use budding yeast FCP1 CTD ======		====== Use budding yeast FCP1 CTD ======
−	We PSI-BLASTed the region right next to BRCT domain of budding yeast FCP1. We found hits in some but not all Saccharomycetales. Meanwhile, the sequences are not very similar to each other. We therefore conclude that budding yeast ~~lack~~ the FCP1 CTD domain.	+	We PSI-BLASTed the region right next to BRCT domain of budding yeast FCP1. We found hits in some but not all Saccharomycetales. Meanwhile, the sequences are not very similar to each other. We therefore conclude that budding yeast lacks the FCP1 CTD domain.
		+
		+	====== Use Dicty FCP1 CTD ======
		+	Dicty has two FCP1s. One has BRCT right at the C-terminal, which means it lacks FCP1 CTD domain. We PSI-BLASTed the region right next to BRCT domain, but there is only one hit except itself, which is a gene of D. purpureum, and the sequence similarity is weak, even cannot make a global alignment. We therefore conclude that Dicty lacks the FCP1 CTD domain.

@@ Line 20: / Line 20: @@
 ====== 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 lacks the FCP1 domain. The full sequence of ''C. elegans'' FCP1 is below:
+We 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 lacks the FCP1 CTD domain. The full sequence of ''C. elegans'' FCP1 is below:
 MDIKFEGNDAECTAGLKKASEGSFVLKDHVLIEFKINGKVAGKIKTPCEGVVTFGKGLKPGIVLNKGQVIATVSECTHAIVIKDMCATCGKDLREKGGRAGQRKEQSTANVSMIHHVPELIVSDTLAKEIGSADENNLITNRKLVLLVDLDQTIIHTSDKPMTVDTENHKDITKYNLHSRVYTTKLRPHTTEFLNKMSNMYEMHIVTYGQRQYAHRIAQILDPDARLFEQRILSRDELFSAQHKTNNLKALFPCGDNLVVIIDDRSDVWMYSEALIQIKPYRFFKEVGDINAPKNSKEQMPVQIEDDAHEDKVLEEIERVLTNIHDKYYEKHDLRGSEEVLLDVKEVIKEERHKVLDGCVIVFSGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDDVTHVVGARYGTQKVYQANRLNKFVVTVQWVYACVEKWLKADENLFQLTKESTPPVGRPLGSKYVNDLANMDTIGKAALADMNNEVDEALSDDEDDGDNEDEDDDGNDVGEDKGDENLEEKQEKNEEEMDDVEQNGSVENQSGDALENETDSTSRGQKRKHCPEMEDEEEESDSDNEDDDTPMSYKALLSDSRKKGRIVPENEDDAVFDVDDEKGHAPANIDEEEDDEDNEDEEVPESDDDDEFEDMAALIERQISDAVDEKDQ

@@ Line 14: / Line 14: @@
 ====== 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. Using the orthologs from gOrtholog database, the profile can find the FCP1 CTD in some nematodes but not all. The full sequence of fruit fly FCP1 is below:
+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. Using the orthologs from gOrtholog database, the profile can find the FCP1 CTD in some nematodes but not all (e.g. CTD is found in Loa Loa and C. japonica). The full sequence of fruit fly FCP1 is below:
 MQNIPDEEGATPSRAPGGVAASGAAEGDDGGGGSGAKNSASGNSNNNTSGGGIIVLRAALGENEARAVINKWRVREGQFVSAAQILFLYQPVGVDAKDAKDAGKPGGDCAIQRYKSQRAGVVKKRLRKEGELLTKGDAILELSECIHTTVIKDMCADCGADLRQNENGQTSEASVPMVHTMPDLKVTQKLAQKLGHDDTRRLLADRKLVLLVDLDQTVIHTTNDTVPDNIKGIYHFQLYGPHSPWYHTRLRPGTAEFLERMSQLYELHICTFGARNYAHMIAQLLDPEGKFFSHRILSRDECFNATSKTDNLKALFPNGDSMVCIIDDREDVWNMASNLIQVKPYHFFQHTGDINAPPGLSKHELDGEGVDFKEITEKHGDKDKTESSSEVKPEDTDKGDNTVTSTSKDDDVNEESVDVFEIEGDAKDPEVSNASSATEAPKEPRDKLNGKTNAEDIVVIDDSSSGSPDAEKAASDGEDVVVIDDNSKESTKAEVPPTPAEKNEVVASSTTSPDEKRPSADADVATTSKTPSLRAPLEGQKQIEIEDPDDYLLYLEVILRNIHKRFYSIYDETTEIPDLKVIVPKIRSEVLRGKNLVFSGLVPTQMKLEQSRAYFIAKSLGAEVKPNIDKEITHLVAVNAGTYKVNAAKKEPAIKVVNANWLWTCAERWEHVEEKLFPLDRKVRNKGRQPPAHCHSPEHVVNYSERSEISPSSSKQQEEQSGNFRETLNPLLVFTNADIESMNKDYETFFESDSSSDEGPVNFENPPMDKKLLKRKREDDNSNRAHDFFTRSDDIMIGAPNLVEVDISSNEEADDNNEKEDDDDEMPSAKFRRGEDLPSDLELGSESNSEKEPEDEDDGEWNMMGAALEREFLGLEDFDM

@@ Line 20: / Line 20: @@
 ====== 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:
+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 lacks the FCP1 domain. The full sequence of ''C. elegans'' FCP1 is below:
 MDIKFEGNDAECTAGLKKASEGSFVLKDHVLIEFKINGKVAGKIKTPCEGVVTFGKGLKPGIVLNKGQVIATVSECTHAIVIKDMCATCGKDLREKGGRAGQRKEQSTANVSMIHHVPELIVSDTLAKEIGSADENNLITNRKLVLLVDLDQTIIHTSDKPMTVDTENHKDITKYNLHSRVYTTKLRPHTTEFLNKMSNMYEMHIVTYGQRQYAHRIAQILDPDARLFEQRILSRDELFSAQHKTNNLKALFPCGDNLVVIIDDRSDVWMYSEALIQIKPYRFFKEVGDINAPKNSKEQMPVQIEDDAHEDKVLEEIERVLTNIHDKYYEKHDLRGSEEVLLDVKEVIKEERHKVLDGCVIVFSGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDDVTHVVGARYGTQKVYQANRLNKFVVTVQWVYACVEKWLKADENLFQLTKESTPPVGRPLGSKYVNDLANMDTIGKAALADMNNEVDEALSDDEDDGDNEDEDDDGNDVGEDKGDENLEEKQEKNEEEMDDVEQNGSVENQSGDALENETDSTSRGQKRKHCPEMEDEEEESDSDNEDDDTPMSYKALLSDSRKKGRIVPENEDDAVFDVDDEKGHAPANIDEEEDDEDNEDEEVPESDDDDEFEDMAALIERQISDAVDEKDQ

@@ Line 8: / Line 8: @@
 ===== 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 [http://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&list_uids=23247 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 full sequence of fruit fly FCP1 is below:
+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

← Older revision		Revision as of 19:01, 15 October 2015
Line 14:		Line 14:


−	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 (0.005) and most of the hits worse the threshold are genes of other families. We then downloaded the sequences and built HMM. The full sequence of fruit fly FCP1 is below:	+	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 full sequence of fruit fly FCP1 is below:

	MQNIPDEEGATPSRAPGGVAASGAAEGDDGGGGSGAKNSASGNSNNNTSGGGIIVLRAALGENEARAVINKWRVREGQFVSAAQILFLYQPVGVDAKDAKDAGKPGGDCAIQRYKSQRAGVVKKRLRKEGELLTKGDAILELSECIHTTVIKDMCADCGADLRQNENGQTSEASVPMVHTMPDLKVTQKLAQKLGHDDTRRLLADRKLVLLVDLDQTVIHTTNDTVPDNIKGIYHFQLYGPHSPWYHTRLRPGTAEFLERMSQLYELHICTFGARNYAHMIAQLLDPEGKFFSHRILSRDECFNATSKTDNLKALFPNGDSMVCIIDDREDVWNMASNLIQVKPYHFFQHTGDINAPPGLSKHELDGEGVDFKEITEKHGDKDKTESSSEVKPEDTDKGDNTVTSTSKDDDVNEESVDVFEIEGDAKDPEVSNASSATEAPKEPRDKLNGKTNAEDIVVIDDSSSGSPDAEKAASDGEDVVVIDDNSKESTKAEVPPTPAEKNEVVASSTTSPDEKRPSADADVATTSKTPSLRAPLEGQKQIEIEDPDDYLLYLEVILRNIHKRFYSIYDETTEIPDLKVIVPKIRSEVLRGKNLVFSGLVPTQMKLEQSRAYFIAKSLGAEVKPNIDKEITHLVAVNAGTYKVNAAKKEPAIKVVNANWLWTCAERWEHVEEKLFPLDRKVRNKGRQPPAHCHSPEHVVNYSERSEISPSSSKQQEEQSGNFRETLNPLLVFTNADIESMNKDYETFFESDSSSDEGPVNFENPPMDKKLLKRKREDDNSNRAHDFFTRSDDIMIGAPNLVEVDISSNEEADDNNEKEDDDDEMPSAKFRRGEDLPSDLELGSESNSEKEPEDEDDGEWNMMGAALEREFLGLEDFDM		MQNIPDEEGATPSRAPGGVAASGAAEGDDGGGGSGAKNSASGNSNNNTSGGGIIVLRAALGENEARAVINKWRVREGQFVSAAQILFLYQPVGVDAKDAKDAGKPGGDCAIQRYKSQRAGVVKKRLRKEGELLTKGDAILELSECIHTTVIKDMCADCGADLRQNENGQTSEASVPMVHTMPDLKVTQKLAQKLGHDDTRRLLADRKLVLLVDLDQTVIHTTNDTVPDNIKGIYHFQLYGPHSPWYHTRLRPGTAEFLERMSQLYELHICTFGARNYAHMIAQLLDPEGKFFSHRILSRDECFNATSKTDNLKALFPNGDSMVCIIDDREDVWNMASNLIQVKPYHFFQHTGDINAPPGLSKHELDGEGVDFKEITEKHGDKDKTESSSEVKPEDTDKGDNTVTSTSKDDDVNEESVDVFEIEGDAKDPEVSNASSATEAPKEPRDKLNGKTNAEDIVVIDDSSSGSPDAEKAASDGEDVVVIDDNSKESTKAEVPPTPAEKNEVVASSTTSPDEKRPSADADVATTSKTPSLRAPLEGQKQIEIEDPDDYLLYLEVILRNIHKRFYSIYDETTEIPDLKVIVPKIRSEVLRGKNLVFSGLVPTQMKLEQSRAYFIAKSLGAEVKPNIDKEITHLVAVNAGTYKVNAAKKEPAIKVVNANWLWTCAERWEHVEEKLFPLDRKVRNKGRQPPAHCHSPEHVVNYSERSEISPSSSKQQEEQSGNFRETLNPLLVFTNADIESMNKDYETFFESDSSSDEGPVNFENPPMDKKLLKRKREDDNSNRAHDFFTRSDDIMIGAPNLVEVDISSNEEADDNNEKEDDDDEMPSAKFRRGEDLPSDLELGSESNSEKEPEDEDDGEWNMMGAALEREFLGLEDFDM