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Based on these data, we assigned the putative one-to-one orthology between O. sativa and Arabidopsis CYPs.
Gp17 is 100%% identical to ORF017 of PA73, but has been assigned the putative function of tail chaperonin due to its similarity to Ab26 tail chaperonin.
Comparing the deduced precursor of Prunus TLPs with the reference TLP amino acid sequences in the Rosaceae and other plants, we assigned the putative signal peptides to deduce the mature protein.
The protein gp37 of DLP1 (100%% identity to ORF035 of PA73) and DLP2 (99%% identity to hypothetical protein in Ab26) have been assigned the putative function of transcriptional regulator due to their similarity to the transcriptional regulator of the Burkholderia phage KL1 [ 33].
This Arabidopsis gene shows a high level of similarity with the orthologous wheat gene TRAES_3B_90F2B79E9 in Clique 7, which was experimentally assigned the putative function " Enoyl-CoA reductase" in a 2010 study focused on changes in properties of wheat leaf cuticle during interactions with Hessian fly [ 50].
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Finally, the algorithm assigns the putative annotation t to all hypothetical proteins whose state was set to +1.
The metadata available for the first five hits, as well as bibliographic information when available, were manually inspected to assign the putative functional classification of the cluster.
They were aligned with the Arabidopsis LEA proteins using ClustalW and an unrooted dendogram was drawn (Additional file 10) assigning the putative LEA proteins to the corresponding Pfam domain/motif groups (Additional file 11).
The identified DCL and AGO genes are distributed on chromosomes 2, 3, 4, 5, 7 and 8 of M. truncatula but more concentrated in chromosomes 2, 3 and 5. To assign the putative M. truncatula DCL and AGO genes a Neighbor-joining phylogenetic tree was generated with the predicted complete protein sequences of M. truncatula and A. thaliana DCLs and AGOs.
There is a high level of synteny between the Z chromosomes of butterfly and moth species thus far sequenced (Bombyx, Mita et al. 2004; Xia et al. 2004; Danaus, Zhan et al. 2011; Heliconius, Dasmahapatra et al. 2012), making it possible to assign the putative physical locations of M. sexta Z and autosomal contigs through orthology to B. mori (Harrison et al. 2012).
Base pair one of this chromosome was assigned within the putative origin of replication.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com