Recent Changes

The human PSMB5 protein sequence was used to query the whale shark predicted protein database (__http://whaleshark.georgiaaquarium.org/__) and results of the BLAST are shown below (Table 1). The top 5 hits had e-values below 1e-06, and the best hit had an e value of 7e -124. The top 5 hits were then used as queries against the human genome database (NCBI BLASTp).
{https://lh3.googleusercontent.com/20D8u4jgutrQmW2igTpY4lOJOkDQdl5asBcHBn1j3W2jV2r3SJSSvChtID2nrHnxFWLLTZL_ZYe1ajd-dz7uP2zqkMtaarJLCyqVZEIW6UO5TYTC824mCf6sa7Csg_Vn56PEJl4}
the predicted WhaleshakeWhale shark protein database.
Two of the top 5 predicted proteins from the BLAST of the whale shark predicted proteins were used as queries against the human protein database. The BLAST of both proteins returned PSMB5 as the best hit. See Table 2 below.
{https://lh6.googleusercontent.com/0kZRaqEbgSKFiAocVa7l-wXoJBkqqc29Zy1XtSogJ_Z_bdd5sOVMn6DOREAxMFpptKv9qzGFQOmRar94kKy-zE_GXxETX2_zieDM663dhBm8_ZCQuQkShxtCPm7Y7OP9prQCV-0}

Proteasome subunit beta type-5 (PSMB5)
This Project
assignment was to conduct genomic identifying possible orthologicalortholog proteins in
Background
are hollow and have openings allow target proteinproteins to enter
Methods
Whale shark predicted orthologs
For each of the whale shark and non-whale shark species, we used the hit with the lowest e-value (using the full human protein sequence as query) to create a phylogenetic tree and multiple sequence alignment. To create the multiple sequence alignment and phylogenetic tree, each of the sequences were input in ClustalW2 with default setting.
Searching for PSMB5 in the Whaleshark
5 hits had had e-values of 7e -124.The-124. The top 5
{https://lh3.googleusercontent.com/20D8u4jgutrQmW2igTpY4lOJOkDQdl5asBcHBn1j3W2jV2r3SJSSvChtID2nrHnxFWLLTZL_ZYe1ajd-dz7uP2zqkMtaarJLCyqVZEIW6UO5TYTC824mCf6sa7Csg_Vn56PEJl4}
Table 1: The best BLASTp human PSMB5 hits against the Whale shark predicted protein database. The Galaxy database was used to BLAST the human PSMB5 protein sequence against the predicted Whaleshake protein database. The ID, e-value, Alignment Length, Predicted protein length, and percent (%) identity of the top 5 hits from that BLAST are displayed.
The BLAST of of both
{https://lh6.googleusercontent.com/0kZRaqEbgSKFiAocVa7l-wXoJBkqqc29Zy1XtSogJ_Z_bdd5sOVMn6DOREAxMFpptKv9qzGFQOmRar94kKy-zE_GXxETX2_zieDM663dhBm8_ZCQuQkShxtCPm7Y7OP9prQCV-0}
Table 2. Top 2 predicted whale shark protein BLASTp hits against human protein database. The top results of each BLASTp are shown here with their e-values, name/descriptions, protein length, and percent (%) identity.
queries, we are confidentbelieve that there is evidence that the human PSMB5 aremay be orthologs.
Protein Domains
nucleophile) domain is constructed of
Human
{https://lh5.googleusercontent.com/JAinyQixS6dSFP8Qg0g5UpqwfJy6WILFtGsc2NY2hZggnRpCZ7uupGA7qttGhF4A3LCX-GVuVi9VKLCs8ilspGhXkY7M6P9gfwRdOnL08RVt1Hl8sHAyaVhf0Abu_01ePLK06p8}
Figure 1. The figure displays the protein domains of the best mouse, yeast, elephant shark, whale shark predicted proteins and human PSMB5 protein hits. The proteins were obtained using the
Orthologs
PSMB5 ortholog may exists in
{https://lh5.googleusercontent.com/6OZEN_Xt2tHFH4VO42_x1td3EZvu371asr47PIAEEJg9XKv_PoHz-540OvkFNgmYNHL5TJHYiBJxjziczvmAEplFIpEtsi7rWD2bS7_Ka4iQp214jqR5eTGKQ-BkAErwnJ51sFY}
Table 3. The table above displays the best hits with human PSMB5 protein BLAST. The human PSMB5 sequence was used in protein BLASTs against the individual species listed above. The Species, name, ID, protein length, and e-value are listed.
Figure 4. The figure above displays a phylogenetic tree of PSMB5 best hits of each of the species listed. The best hits from BLASTp searches of the protein databases for individual species and the best whale shark predicted protein were used to create the phylogenetic tree. The ClustalW site was used to generate the tree/image.
Conclusion
and reciprocal BLAStsBLASTs, there is whale shark (i.e Elephant shark) against the
References
“Proteasome Subunit Beta Type-5.” PSMB5. N.p., Web. 31 Mar. 2015.__http://www.uniprot.org/uniprot/P28074__

{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/tree_upgma.png} Figure 2.This is a phylogenetic tree (nonproportional branch lengths) made mostly with best-hit orthologs from other organisms to the human POMP sequence. Hit 1 and Hit 2 show the only two hits found when BLASTing the human POMP sequence against the whaleshark genome. "Human match on Zebrafish proteome" shows the phylogeny of a zebrafish ortholog to the human POMP sequence. This was done by BLASTing the human POMP sequence against the zebrafish proteome (as opposed to genome). "Possible whaleshark ortholog" shows the relative phylogeny of the best-hit protein sequence on the whaleshark genome when the zebrafish ortholog was blasted against it. This is a bootstrapping technique done through the zebrafish genome.
{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/treebl_upgma.png} Figure 3.Phylogenetic tree with proportional branch lengths. Shows the same possible orthologs as Figure 2.
Alignment from this analysis is shown below:
<span style="color: #000000; font-family: monospace; font-size: 12px;">CLUSTAL 2.1 multiple sequence alignment
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote MARRKVPLLLHGFLLLVLCRSSLQGGPFVKPPKTGGYGGLPGIGAGGTGV
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GLGGLGLRPAGPGVGGLVPGGFGVGTGVGGTGTGVPAIGVGTGVGGLGIG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GVGPGGAGIGVSTGGIGPGGVVPGGIRPGGIVPGGVGPGGIVPGGVGPGG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote IFPGGVGPGGIVPGGVGPGGIVPGGVGPGGIVPGGVGPGGIVPGAGRKPG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote KPGYVGPGGGAGPFGTGTLGAGDPRFGAIPLTPGGTGTGYPSGGGYGGYG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GPGGIYPGAAGQKPPKPGIGPGGTGTGLGGAGFGLGGAGVRPGGVGIGPG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GTGIGSGGTGLGPGGTGVGTGGVGIGPGGTGTGGVGIAPGGSSFLPQTGL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote PGIGPGTGGKVGKPGKAPVPGAAKSQAKAAKYGAAGVPGLGGGLGVGGVP
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GAGGITGTSGVPGLGGVPGAGTVPGIGSVPGAAGIPGVGGIPGAGGATPG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GLYPGAGGIYPGASGVGTGGLPGSGVGLGGLGTGGLPGSGVGVGGLGTGG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote LPGSGVGVGGLGTGGLPGSGVGVGGLGTGGLPGSGLGGGGLGAGGLPGSG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote VGGGGLGAGGLPGSGISPEAQLGRGGTLGTGGLPGGAAGVGLPGGGLGAG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GQLGTGGLGTYGLPGGGLGGLPGGGAGGLPVGGIGGLPGSGTAQLGRGGT
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote LGTGGLPGGTAGVGLPGGGLGAGGQLGGGLGTGGLPGGGLGTGGQLGGGL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GTGGLPRGGLGTGGQLGGGIGTGGLGTGGLPTGGLGGLPGGGVGGLPGGG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote IGGLPGSGIGTRLYNHIALNKFILRFHAQLGRGGTLGSGGLPGGTAGVGL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GGLPGGGLGTGGQLGGGLGTGGLPGGGLGGLPGGGAGGLPGYAEAKARKY
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote AQLGRGGTLGTGGLPGGAAGVGLGGLPGGGLGTGGQLGGGLGTGGLGTGL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GGLPGGGAGGLPSGGVGGLPGLLGRGTGLGPGTGLAAGIPGGLPSTGIAP
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GGAGGLPGSGVGQGGIPGVGYGSGGAPSGGFGPGSVPGGGYGPGGISAAK
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote ARKYGIIAGAGGVGLPGGQLGSGTVPGVGAGGGTPVAGIGPGGVPVGGYR
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote PGGVPAGGYGPGGVPAGGYGPGGVPAGGYGPGGVPAGGYGPGGVPAGGYG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote PGGVPAGGFGQGSGGPGGSGGIPGLGLQGQVGTGPAGGLGTGAGQVGGFG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote PGTLGGPGSGFAGSGLPGSAVGAGSRGGLGPGYGTGAGGLPGFGGALGTG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote ALPGAGTGAGGQPVGGVGSVPSGSVPATGGTGVTGTGISTGGTAIPLATG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote TDRGGLRPGGVTGGPIDTDGLYGVAGTGIPILAGERPGGTGVPRPESTGG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GAIAGRGDTPGTIEGGPGSIGSGIGGVGGGPGGVGATPVYGGAGGTGALG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote VGGVGGLGPAGGGGAGLLPGGGGLLPGGGAAGTGFGLQKPGKIYGAGTLG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GLGGPGGYGAGPGGYGGGPGGYGSGPGSAGGLGGPGFGASKFTITNLFGL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote SGYGGAGALGGAGQGGIGGGPGRLGVGPGGAGGIGGGLGVGPGGVGGGPG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GLGGGFGGYGGVGGGPGGTGGGNNIRFYAALSDELHHARCCECNSVLADW
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote YYERDGQFFCKKHYLSRFAEQCYGCTESINTGPIMWSMSLPEGVDTAFGS
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote KRFTASSYGDIDVISSLCRKQTRFILHCGEERQRAFGHCFSINLVIHDTE
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote HWLQITIEHNPKDHIKQEDLSGLLGEELDQPGNLGFFPLPNNRQISHRSK
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote NILRSCSIDKVPCLQRHAALLSHRRDINRSESLRFDANDKTQRIFRPSDL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote IYGEILGKGCFGQAIKVKVMRCLEHPNVLKFIGILYKDKRLNLISEYVQG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GTLRDTILKMNQTVVVADFGLAQLVKDEKTSSPGQMSKLNKLGRKKRYTV
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote VGNPYWMAPEMINGKIYDERVDIFSFGIVLCEIIGRVYADPDFLPRTQEY
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GLNVKEFLERCWSKDCPAAFFPIAVLCCALEAEKRPVFAKLEEWLENVMM
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote HLEMGLPLMSELLKFSIGLPDSGMESFLRDVDTSLESTQAEDKDKNIFPS
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote EALCSSSPLAEHKTRPVDDHGLPVRGQSHWGHFDPYDDSEECVGIVTLPN
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 -----------------------------MLSDFKYVLGFRARILENVDT
Human ------------MNARGLGSELKDSIPVTELSASGP-FESHDLLRKGFSC
Sumatran_Orangutan ------------MNARGLGSELKDSIPVTELSASGP-FESHDLLRKGFSC
Chimpanzee ------------MNARGLGSELKDSIPVTELSASGP-FESHDLLRKGFSC
Western_Clawed_Frog ------------MNTKALGSQLKDSIPIGELSTQYGGYGVHDNLRTGFTS
Downy_Woodpecker ------------MNTKALGSQLKDSIPIGELSTQYGGYGVHDNLRTGFTS
Elephant_Fish ------------MNTRGLRSEMKESIPG-ELNPYAESFGVHDTLRRGFTN
Zebra_Fish ------------MNTRGLRSQLKDSVPVTGLCPQAGPYGVQDSLRRGFSS
American_Crow ---------MIFCAEGTLYFCLLNCVTDSVELRYMLKVGFLQKFLGGFTS
Human_match_on_Zebrafish_prote QVKYKAVKRGFVFNLMVVGESGLGKSTLVDTLFLTNLYMDRHIPVASEKI
Possible_Whaleshark_Ortholog_g ------------------------------------------------RI
Hit_1_g26661.t1 --------------------MLMGLRADSRSEQKMATSSVYREALTGWAL
Hit_2_g47082.t1 LTTGGGQPIGDKLNVMTAGPRGPLLMQDTVFVDEMAHFDRERIPERVVHA
Human VKNELLPSHPLELSEKNFQLNQDKMNFSTLRN---IQGLFAPLKLQMEFK
Sumatran_Orangutan VKNELLPSHPLELSEKNFQLNQDKMNFSTLRN---IQGLFAPLKLQMEFK
Chimpanzee VKNELLPSHPLELSEKNFQLNQDKMNFSTLRN---IQGLFAPLKLQMEFK
Western_Clawed_Frog VRSELMPSHPLELSEKNFQINQEKVNLSTVRN---IQGLHAPLKLQMEFK
Downy_Woodpecker VRSELMPSHPLELSEKNFQINQEKVNLSTVRN---IQGLHAPLKLQMEFK
Elephant_Fish VKSELLPSHPLEISEKNFQLTQDKVNFTTLRN---IQGLHAPLKLQMEYK
Zebra_Fish VKNELLPSHPLELSEKNFQLNQDKMNFNTLRN---IQGLHAPLKLQMEYR
American_Crow VKNELLPSHPLELTEKNFQLNQDKTNFARLRN---VQGIHAPLKLQMEFR
Human_match_on_Zebrafish_prote ARTVSITKSTVDIVEEGVNLRLTVIDTPGFGD---ALDNRESWKAALRYV
Possible_Whaleshark_Ortholog_g TQTVDITKHSVEIEEKGVRLRLTIIDTPGFGD---AINNQECWKPIADYI
Hit_1_g26661.t1 LPGIVTP-----LRLASFLLDTAKGCVQHTNK---QSDPMADSLPEAHFG
Hit_2_g47082.t1 KGAEQYERVMEQMWYIRVNNPWSPLCLGQTGGGPIVLGLIILYDTPLEQM
: . .
Human AVQQVQRLPFLSSS--NLSLDVLRGNDETIGFEDILNDPSQSEVMGEPHL
Sumatran_Orangutan AVQQVQRLPFLSSS--NLSLDVLRGNDETIGFEDILNDPSQSEVMGEPHL
Chimpanzee AVQQVQRLPFLSSS--NLSLDVLRGNDETIGFEDILNDPSQSEVMGEPHL
Western_Clawed_Frog AVRQVQRLPFLPSS--NIALDTLRGTDESIGFEDILNDPSQSEGMGEPHL
Downy_Woodpecker AVRQVQRLPFLPSS--NIALDTLRGTDESIGFEDILNDPSQSEGMGEPHL
Elephant_Fish AVQQVQRLPFLMSS--NIALETLRGSDECIGFEDVLNDPSQSEFMGEPHL
Zebra_Fish AAKQIQRLPFLPSS--NLALDTLRGSDDTIGFEDILNDPVQCEMMGDPHI
American_Crow AVKQVQRLPFLHSS--NMAMDILRGNDECIGFEDILNDPSQSEVMGEPHM
Human_match_on_Zebrafish_prote NQQMVKYYKDEVGV--NRQNIKDNRVHCCLYFISPHGHGLRPIDVKFMKA
Possible_Whaleshark_Ortholog_g DQQFEQYFRDESGV--NRKNIVDNRIHCCLYFISPFGH------------
Hit_1_g26661.t1 ESAPHERVDILSKT--FSWFRLMR----------------QAPIPPYP--
Hit_2_g47082.t1 GLQLRTSGPEVETLPLVRKGPNLVTNHLVPSCRTNSIKGYYSNVEKLQHA
Human MVEYKLGLL-----------------------------------------
Sumatran_Orangutan MVEYKLGLL-----------------------------------------
Chimpanzee MVEYKLGLL-----------------------------------------
Western_Clawed_Frog MMEYKLGLL-----------------------------------------
Downy_Woodpecker MMEYKLGLL-----------------------------------------
Elephant_Fish MMEYKLGLL-----------------------------------------
Zebra_Fish MTEYKLGLL-----------------------------------------
American_Crow MMEHKLGLL-----------------------------------------
Human_match_on_Zebrafish_prote LEQKVNIVPVLAKADSLTQKETRNMKAKVRMSLTEKLRKSRVCRWCWDAL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 AVQRDLGVPVHESQKVGLQVEQELR-------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote DWNASELTSGGFRQDTMLGKDYMLAIIIVNYDDNIWNDQSLELDSDLPPG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote WRTIRDSTGTYYWHVPTGTTQWQHPSYSAEEEQNAINGVTASQIKLAADG
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote RRESRGRLTENPLPSLSERPSWQEEYFCANMDPDSKCFAVRSLGWVEIPE
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote EELTPGKSSLAVNNCIQQLSHSKAEGRDAEGAWGEDMMMVLKKDTLSLMD
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote PVDQSLIHCQPIINIRVWGVGCNNGRDFAFVASDKDTCMLKCHVFRCNAP
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote AKTIASALHEMCSKTPLCISQFLIVIGVFEQIMTEKAALQPSMARSLTME
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote SISPEDLPRQGMEVLNRAIESIMHSRDRDEWEPIVIHVSDTVLSLWRGED
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GDDPFWESQVRYLTFLGVGHDTHTFAVIVDAGTQRFECHVFWCEPDAGII
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote SEAVQAACMVQYQKCLVAQTPPVRPKIWRAGSKVKRANSMDGSSFPPRYQ
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote GHTASKMTSPSVKKGMLAFFETFRNKHSANTRGLRSQLKDSVPVTGLCPQ
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human --------------------------------------------------
Sumatran_Orangutan --------------------------------------------------
Chimpanzee --------------------------------------------------
Western_Clawed_Frog --------------------------------------------------
Downy_Woodpecker --------------------------------------------------
Elephant_Fish --------------------------------------------------
Zebra_Fish --------------------------------------------------
American_Crow --------------------------------------------------
Human_match_on_Zebrafish_prote AGPYGVQDSLRRGFSSVKNELLPSHPLELSEKNIQRLPFLPSSNLALDTL
Possible_Whaleshark_Ortholog_g --------------------------------------------------
Hit_1_g26661.t1 --------------------------------------------------
Hit_2_g47082.t1 --------------------------------------------------
Human ------------------------------------
Sumatran_Orangutan ------------------------------------
Chimpanzee ------------------------------------
Western_Clawed_Frog ------------------------------------
Downy_Woodpecker ------------------------------------
Elephant_Fish ------------------------------------
Zebra_Fish ------------------------------------
American_Crow ------------------------------------
Human_match_on_Zebrafish_prote RGSDDTIGFEDILNDPVQCEMMGDPHIMTEYKLGLL
Possible_Whaleshark_Ortholog_g ------------------------------------
Hit_1_g26661.t1 ------------------------------------
Hit_2_g47082.t1 ------------------------------------</span>
Conclusions
Bootstrapping through the zebrafish proteome resulted in a protein that was phylogenetically further from human POMP than the first hit from the direct BLAST search. Therefore, it was concluded that g26661.t1 is the closest whale shark ortholog to the human POMP gene. However, given the unpromising e-values, it is not believed that it is a very closely-related ortholog. Like this project on Facebook (below the page title)!

{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/treebl_upgma.png} Figure 3.Phylogenetic tree with proportional branch lengths. Shows the same possible orthologs as Figure 2.
Conclusions
closely-related ortholog. Like this project on Facebook (below the page title)!
References
Adams, J. "The Proteasome: Structure, Function, And Role In The Cell." Cancer Treatment Reviews (2003): 3-9. Pub Med. Web. 14 Apr. 2015.

2382
56.03
these results.
Whale Shark ID
E-Value

102
31.71
It was concluded that there was not enough evidence of a whaleshark ortholog based on the e-values and %identity. Therefore, a bootstrapping technique was used. The human POMP protein was BLASTed against the zebrafish proteome, producing one relatively convincing ortholog among 14 total hits, shown below.
Zebrafish ID
E-Value
Alignment Length
Predicted Protein Length
% Identity
danRer7_genscan_chr21.1483_1
1e-45
141
2382
56.03
This protein had an e-value of 1e-45, which was significantly lower than the other hits which had e-values ending in the e-4 and e-5 range. This protein was sequenced using Galaxy's FASTA sequence extract tool and blasted against the whale shark genome, producing these results.
Whale Shark ID
E-Value
Alignment Length
Predicted Protein Length
% Identity
g28889.t1
3e-39
85
2832
63.53
Based on this bootstrapping technique, it can be concluded that g28889.t1 protein found in whale sharks can be orthologous to human POMP.
Protein domains
The POMP protein is part of the UMP1 superfamily of proteins.
{http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?SEQUENCE=5106990&JUSTPIC} Figure 1. Putative domains of the human POMP gene BLASTed against the human genome, showing complete association with its superfamily. The UMP1 superfamily is the superfamily of genes associated with the POMP gene.
Orthologs
Based on the boostrapping technique outlined above and the direct BLAST searches, there were three possible whale shark orthologs to human POMP:
g47082.t1
g26661.t1
g28889.t1
CLUSTALW was used to analyze the alignment of these sequences, as well as
best-hit orthologs from other organisms, shown below.
Phylogeny
{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/tree_upgma.png} Figure 2.This is a phylogenetic tree (nonproportional branch lengths) made mostly with best-hit orthologs from other organisms to the human POMP sequence. Hit 1 and Hit 2 show the only two hits found when BLASTing the human POMP sequence against the whaleshark genome. "Human match on Zebrafish proteome" shows the phylogeny of a zebrafish ortholog to the human POMP sequence. This was done by BLASTing the human POMP sequence against the zebrafish proteome (as opposed to genome). "Possible whaleshark ortholog" shows the relative phylogeny of the best-hit protein sequence on the whaleshark genome when the zebrafish ortholog was blasted against it. This is a bootstrapping technique done through the zebrafish genome.
{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/treebl_upgma.png} Figure 3.3.Phylogenetic tree with proportional branch lengths. Shows the same possible orthologs as Figure 2.
Conclusions
Bootstrapping through the zebrafish proteome resulted in a protein that was phylogenetically further from human POMP than the first hit from the direct BLAST search. Therefore, it was concluded that g26661.t1 is the closest whale shark ortholog to the human POMP gene. However, given the unpromising e-values, it is not believed that it is a very closely-related ortholog.
References
Adams, J. "The Proteasome: Structure, Function, And Role In The Cell." Cancer Treatment Reviews (2003): 3-9. Pub Med. Web. 14 Apr. 2015.

Protein domains
The POMP protein is part of the UMP1 superfamily of proteins.
with its own sequence.superfamily. The UMP1 superfamily
Orthologs
Phylogeny
<span style="color: #000000; font-family: monospace; font-size: 12px;">CLUSTAL 2.1 multiple{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/tree_upgma.png} Figure 2.This is a phylogenetic tree (nonproportional branch lengths) made mostly with best-hit orthologs from other organisms to the human POMP sequence. Hit 1 and Hit 2 show the only two hits found when BLASTing the human POMP sequence alignment
Human ---MNARGLGSELKDSIPVTELSASG-PFESHDLLRKGFSCVKNELLPSHPLELSEKNFQ
Sumatran-Orangutan ---MNARGLGSELKDSIPVTELSASG-PFESHDLLRKGFSCVKNELLPSHPLELSEKNFQ
Chimpanzee ---MNARGLGSELKDSIPVTELSASG-PFESHDLLRKGFSCVKNELLPSHPLELSEKNFQ
Western-Clawed-Frog ---MNTKALGSQLKDSIPIGELSTQYGGYGVHDNLRTGFTSVRSELMPSHPLELSEKNFQ
Downy-Woodpecker ---MNTKALGSQLKDSIPIGELSTQYGGYGVHDNLRTGFTSVRSELMPSHPLELSEKNFQ
Elephant-Fish ---MNTRGLRSEMKESIPG-ELNPYAESFGVHDTLRRGFTNVKSELLPSHPLEISEKNFQ
Zebra-Fish ---MNTRGLRSQLKDSVPVTGLCPQAGPYGVQDSLRRGFSSVKNELLPSHPLELSEKNFQ
American-Crow MIFCAEGTLYFCLLNCVTDSVELRYMLKVGFLQKFLGGFTSVKNELLPSHPLELTEKNFQ
* : :.:. : : **: *:.**:******::*****
Human LNQDKMNFSTLRNIQGLFAPLKLQMEFKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFED
Sumatran-Orangutan LNQDKMNFSTLRNIQGLFAPLKLQMEFKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFED
Chimpanzee LNQDKMNFSTLRNIQGLFAPLKLQMEFKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFED
Western-Clawed-Frog INQEKVNLSTVRNIQGLHAPLKLQMEFKAVRQVQRLPFLPSSNIALDTLRGTDESIGFED
Downy-Woodpecker INQEKVNLSTVRNIQGLHAPLKLQMEFKAVRQVQRLPFLPSSNIALDTLRGTDESIGFED
Elephant-Fish LTQDKVNFTTLRNIQGLHAPLKLQMEYKAVQQVQRLPFLMSSNIALETLRGSDECIGFED
Zebra-Fish LNQDKMNFNTLRNIQGLHAPLKLQMEYRAAKQIQRLPFLPSSNLALDTLRGSDDTIGFED
American-Crow LNQDKTNFARLRNVQGIHAPLKLQMEFRAVKQVQRLPFLHSSNMAMDILRGNDECIGFED
:.*:* *: :**:**:.********::*.:*:****** ***:::: ***.*: *****
Human ILNDPSQSEVMGEPHLMVEYKLGLL
Sumatran-Orangutan ILNDPSQSEVMGEPHLMVEYKLGLL
Chimpanzee ILNDPSQSEVMGEPHLMVEYKLGLL
Western-Clawed-Frog ILNDPSQSEGMGEPHLMMEYKLGLL
Downy-Woodpecker ILNDPSQSEGMGEPHLMMEYKLGLL
Elephant-Fish VLNDPSQSEFMGEPHLMMEYKLGLL
Zebra-Fish ILNDPVQCEMMGDPHIMTEYKLGLL
American-Crow ILNDPSQSEVMGEPHMMMEHKLGLL
:**** *.* **:**:* *:*****</span>
{treebl_upgma.pdf} against the whaleshark genome. "Human match on Zebrafish proteome" shows the phylogeny of a zebrafish ortholog to the human POMP sequence. This was done by BLASTing the human POMP sequence against the zebrafish proteome (as opposed to genome). "Possible whaleshark ortholog" shows the relative phylogeny of the best-hit protein sequence on the whaleshark genome when the zebrafish ortholog was blasted against it. This is a bootstrapping technique done through the zebrafish genome.
{http://www.genome.jp/tmp/clustalw/150422062200DbhaO/treebl_upgma.png} Figure 3.
Conclusions
References

Orthologs
Phylogeny
<span style="color: #000000; font-family: monospace; font-size: 12px;">CLUSTAL 2.1 multiple sequence alignment
Human ---MNARGLGSELKDSIPVTELSASG-PFESHDLLRKGFSCVKNELLPSHPLELSEKNFQ
Sumatran-Orangutan ---MNARGLGSELKDSIPVTELSASG-PFESHDLLRKGFSCVKNELLPSHPLELSEKNFQ
Chimpanzee ---MNARGLGSELKDSIPVTELSASG-PFESHDLLRKGFSCVKNELLPSHPLELSEKNFQ
Western-Clawed-Frog ---MNTKALGSQLKDSIPIGELSTQYGGYGVHDNLRTGFTSVRSELMPSHPLELSEKNFQ
Downy-Woodpecker ---MNTKALGSQLKDSIPIGELSTQYGGYGVHDNLRTGFTSVRSELMPSHPLELSEKNFQ
Elephant-Fish ---MNTRGLRSEMKESIPG-ELNPYAESFGVHDTLRRGFTNVKSELLPSHPLEISEKNFQ
Zebra-Fish ---MNTRGLRSQLKDSVPVTGLCPQAGPYGVQDSLRRGFSSVKNELLPSHPLELSEKNFQ
American-Crow MIFCAEGTLYFCLLNCVTDSVELRYMLKVGFLQKFLGGFTSVKNELLPSHPLELTEKNFQ
* : :.:. : : **: *:.**:******::*****
Human LNQDKMNFSTLRNIQGLFAPLKLQMEFKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFED
Sumatran-Orangutan LNQDKMNFSTLRNIQGLFAPLKLQMEFKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFED
Chimpanzee LNQDKMNFSTLRNIQGLFAPLKLQMEFKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFED
Western-Clawed-Frog INQEKVNLSTVRNIQGLHAPLKLQMEFKAVRQVQRLPFLPSSNIALDTLRGTDESIGFED
Downy-Woodpecker INQEKVNLSTVRNIQGLHAPLKLQMEFKAVRQVQRLPFLPSSNIALDTLRGTDESIGFED
Elephant-Fish LTQDKVNFTTLRNIQGLHAPLKLQMEYKAVQQVQRLPFLMSSNIALETLRGSDECIGFED
Zebra-Fish LNQDKMNFNTLRNIQGLHAPLKLQMEYRAAKQIQRLPFLPSSNLALDTLRGSDDTIGFED
American-Crow LNQDKTNFARLRNVQGIHAPLKLQMEFRAVKQVQRLPFLHSSNMAMDILRGNDECIGFED
:.*:* *: :**:**:.********::*.:*:****** ***:::: ***.*: *****
Human ILNDPSQSEVMGEPHLMVEYKLGLL
Sumatran-Orangutan ILNDPSQSEVMGEPHLMVEYKLGLL
Chimpanzee ILNDPSQSEVMGEPHLMVEYKLGLL
Western-Clawed-Frog ILNDPSQSEGMGEPHLMMEYKLGLL
Downy-Woodpecker ILNDPSQSEGMGEPHLMMEYKLGLL
Elephant-Fish VLNDPSQSEFMGEPHLMMEYKLGLL
Zebra-Fish ILNDPVQCEMMGDPHIMTEYKLGLL
American-Crow ILNDPSQSEVMGEPHMMMEHKLGLL
:**** *.* **:**:* *:*****</span>
{treebl_upgma.pdf}
Conclusions
References

Table 1. Human ERAP 2 gene best hits in the Whaleshark Genome. These 6 hits had the lowest e-values and therefore were deemed the
closest matches contained within the whaleshark genome.4
from zero). Therefore we decided that a bootstrapping ofAlso, when blasted back against the human gene againstgenome, the elephanttop whale shark genomehit produces a human gene moderately similar to ERAP2, but not homologous. Therefore a bootstrapping technique was necessaryused in an attempt to obtain possibly more accurateget better results.
Bootstrapping:
Human ERAP2 gene is blasted against an organism more similar to the whale shark, like the elephant shark. The top hit from this blast is then blasted against the whale shark genome to see if results change.
Description
Max
97
Table 3. Exhibits the best hits of the elephant shark ERAP2 gene when blasted on the whale shark genome.
gene g29177.t1.
Conserved Domain:
{http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?dhandle=QM3-data_cache-62B81B29D3C3668-553146E570BB6&show_feat=true&mode=std&gwidth=900&output=graph}

ERAP2 (ENSP00000400376)
Background
The human protein sequence (ENSP00000400376) was used as the query in a Blast. This query was placed against the predicted whale shark protein database which was found in the whaleshark.georgiaaquarium.org Galaxy server. The top 5 predicted protein hits were used as queries in protein BLASTs against the NCBI human protein database.
Predicted Orthologs
elephant shark, elephat, yeast, and
.
Phylogenetic tree
Table 1. Human ERAP 2 gene best hits in the Whaleshark Genome. These 6 hits had the lowest e-values and therefore were deemed the
closest matches contained within the whaleshark genome.4
of the human gene against the elephant shark genome was necessary to obtain possibly more accurate results.
Bootstrapping:
Description
Max
Score
Total
Score
Query
Cover
E-value
% ID
PREDICTED: endoplasmic reticulum aminopeptidase 2 [Callorhinchus milii]
1092
1092
87%
0.0
60%
Table 2. Shows the best hit for the human ERAP2 gene in the Elephant Shark genome.
This best hit shown above was then blasted against the whaleshark database to see if better results (e-values) would be obtained.
Sequence ID
E-value
% ID
Alignment Length
Query Coverage
g34464.t1
9e-24
80.77%
52
91
g29177.t1
3e-23
76.67%
60
97
Table 3. Exhibits the best hits of the elephant shark ERAP2 gene when blasted on the whale shark genome.
These two best hits were also the top two when the human ERAP2 gene was blasted on the whale shark genome. In comparison between the two, the elephant shark actually gave worse values for the best hit gene g34464.t1, but gave better values for the gene g29177.t1.
Conserved Domain:
Conclusion:
Finding best hits for the ERAP2 gene{http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?dhandle=QM3-data_cache-62B81B29D3C3668-553146E570BB6&show_feat=true&mode=std&gwidth=900&output=graph}
Figure 2. Conserved domains in the whaleshark genome confirmed that the whaleshark does have the ERAP2 gene within its genome. However,gene.
Phylogenetic Tree:
Orthologues
Organism
Protein
E-value
query coverage (%)
% ID
Mouse
ERAP1
0.0
94.30
51.22
Zebrafish
ERAP2
0.0
95.00
58.46
Rabbit
ERAP1
0.0
94.56
53.32
Elephant
ERAP2
0.0
99.68
80.36
Yeast
APE2
3e-128
94.26
30.75
Table 4. Human ERAP2 gene blasted against other organisms to get values for comparison in a phylogenetic tree. Values in table are best hits for each organism.
{http://www.genome.jp/tmp/clustalw/1504180410152OkB3/tree_upgma.png}
Figure 3. A tree diagram of all the organisms best hits against the human ERAP2 gene highlights similarities between organisms.
Conclusion:
Finding best hits for the ERAP2 gene in the whale shark genome confirmed that the whale shark may have a similar gene to that of the human ERAP2 gene; however, when blasted back against the human genome, the results indicate that the whale shark gene g34464.t1 is not a homologue to ERAP2. This is further evidenced using bootstrapping techniques where the human ERAP2 gene was blasted against the elephant shark genome, which produced a homologous gene. This gene was then blasted against the whaleshark genome, but gave similar results to the human blast. It may be that the whale shark has genes that are distantly similar and produce proteins that perform distantly similar tasks, but are not homologous to ERAP2. The conclusion is that whale sharks do not have a homologous gene to ERAP2.
Works Cited:
Evnouchidou, I., M. Weimershaus, L. Saveanu, and P. Van Endert. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 31 Mar. 2015.