Phosphatase Subfamily FCP1 Tech Notes

Phosphatase Classification: Fold HAD: Superfamily HAD: Family FCP: Subfamily FCP1: Technical Notes

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. 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

Use C. elegans FCP1 CTD

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

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 lacks the FCP1 CTD domain.

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.

Sponge and Monosiga have a single FCP1 for each. We PSI-BLASTed the region right next to BRCT domain, but it resulted in no significant hit except itself. We therefore conclude that sponge and monosiga lacks the FCP1 CTD domain.