Difference between revisions of "Phosphatase Subfamily FCP1 Tech Notes"
| Line 2: | Line 2: | ||
==== FCP1_C domain ==== | ==== FCP1_C domain ==== | ||
| + | ===== Using Pfam profile ===== | ||
In order to find FCP1_C domain phylogenetic distribution among FCP1, we obtained the FCP1 from our [http://resdev.gene.com/gOrtholog/view/cluster/MC0001572/overview internal orthology database], which contains 227 from 183 eukaryotic genomes. We then searched the FCP1_C domain by Pfam web server. | In order to find FCP1_C domain phylogenetic distribution among FCP1, we obtained the FCP1 from our [http://resdev.gene.com/gOrtholog/view/cluster/MC0001572/overview 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. | 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 ===== | ||
| + | |||
| + | PSI-BLAST the FCP1_C region (716-961 as defined by CDD): | ||
| + | |||
| + | MEVPAAGRVPAEGAPTAAVAEVRCPGPAPLRLLEWRVAAGAAVRIGSVLAVFEAAASAQSSGASQSRVASGGCVRPARPERRLRSERAGVVRELCAQPGQVVAPGAVLVRLEGCSHPVVMKGLCAECGQDLTQLQSKNGKQQVPLSTATVSMVHSVPELMVSSEQAEQLGREDQQRLHRNRKLVLMVDLDQTLIHTTEQHCQQMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTGNLRNLFPCGDSMVCIIDDREDVWKFAPNLITVKKYVYFQGTGDMNAPPGSRESQTRKKVNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPEGAGALAQGSSLEPGRPAAPSLPGEAEPGAHAPDKEPELGGQEEGERDGLCGLGNGCADRKEAETESQNSELSGVTAGESLDQSMEEEEEEDTDEDDHLIYLEEILVRVHTDYYAKYDRYLNKEIEEAPDIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHATALGAKILTRLVLSPDAPDRATHLIAARAGTEKVLQAQECGHLHVVNPDWLWSCLERWDKVEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGKLIRTGARGPPAPSSSLPIRQEPSSFRAVPPPQPQMFGEELPDAQDGEQPGPSRRKRQPSMSETMPLYTLCKEDLESMDKEVDDILGEGSDDSDSEKRRPEEQEEEPQPRKPGTRRERTLGAPASSERSAAGGRGPRGHKRKLNEEDAASESSRESSNEDEGSSSEADEMAKALEAELNDLM | ||
Revision as of 17:38, 15 October 2015
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
PSI-BLAST the FCP1_C region (716-961 as defined by CDD):
MEVPAAGRVPAEGAPTAAVAEVRCPGPAPLRLLEWRVAAGAAVRIGSVLAVFEAAASAQSSGASQSRVASGGCVRPARPERRLRSERAGVVRELCAQPGQVVAPGAVLVRLEGCSHPVVMKGLCAECGQDLTQLQSKNGKQQVPLSTATVSMVHSVPELMVSSEQAEQLGREDQQRLHRNRKLVLMVDLDQTLIHTTEQHCQQMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTGNLRNLFPCGDSMVCIIDDREDVWKFAPNLITVKKYVYFQGTGDMNAPPGSRESQTRKKVNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPEGAGALAQGSSLEPGRPAAPSLPGEAEPGAHAPDKEPELGGQEEGERDGLCGLGNGCADRKEAETESQNSELSGVTAGESLDQSMEEEEEEDTDEDDHLIYLEEILVRVHTDYYAKYDRYLNKEIEEAPDIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHATALGAKILTRLVLSPDAPDRATHLIAARAGTEKVLQAQECGHLHVVNPDWLWSCLERWDKVEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGKLIRTGARGPPAPSSSLPIRQEPSSFRAVPPPQPQMFGEELPDAQDGEQPGPSRRKRQPSMSETMPLYTLCKEDLESMDKEVDDILGEGSDDSDSEKRRPEEQEEEPQPRKPGTRRERTLGAPASSERSAAGGRGPRGHKRKLNEEDAASESSRESSNEDEGSSSEADEMAKALEAELNDLM
