Identify protein sequences from L.infantum with more than 60% conservancy with other Leishmania species

Question

[dzisis1986]

I downloaded the available proteomes (from L. braziliensis, Leishmania major, and L. infantum) from TriTrypDB and i want to use them in order to take only protein sequences from L.infantum with more than 60% conservancy with other Leishmania species verified through BLAST protein alignment. I am using Blastp in command line and up to now i manage to take only the two top sequences with this :

blastp -query Linfantum.prot.fasta -db /home/dimitris/blastdb/db/blast/Lbraziliensis.prot.fasta -evalue 1e-3 -outfmt '6 qseqid sseqid qlen length evalue' -max_target_seqs 2 -comp_based_stats F -out Linfantum_vs_Lbraziliensis_seq_newest.txt

Do you know which parameter i have to use in order to achieve 60% of conservancy between Linfantum and Lbraziliensis by using Blastp ?

[GenoMax]

You will need to post process the results to get this type of information. There isn't a simple parameter that will do that.

[dzisis1986]

this is a sample result of my blastp :

LinJ_31_3340_mRNA   LbrM_31_2880_mRNA   824 793 0.0
LinJ_31_3340_mRNA   LbrM_31_2870_mRNA   824 438 0.0
LinJ_31_3350_mRNA   LbrM_31_2870_mRNA   468 468 0.0
LinJ_31_3350_mRNA   LbrM_31_2880_mRNA   468 469 0.0
LinJ_34_4350_mRNA   LbrM_08_1110_mRNA   193 169 3e-57
LinJ_34_4350_mRNA   LbrM_08_1140_mRNA   193 168 4e-57
LinJ_34_4360_mRNA   LbrM_14_1300_mRNA   336 337 0.0
LinJ_34_4360_mRNA   LbrM_20_1430_mRNA   336 167 2e-82
LinJ_34_4370_mRNA   LbrM_08_1100_mRNA   185 182 4e-64
LinJ_34_4370_mRNA   LbrM_08_1090_mRNA   185 174 2e-63
LinJ_34_4380_mRNA   LbrM_20_3960_mRNA   113 113 7e-83
LinJ_34_4380_mRNA   LbrM_20_3940_mRNA   113 113 7e-83
LinJ_34_4390_mRNA   LbrM_20_3950_mRNA   221 221 1e-144
LinJ_34_4390_mRNA   LbrM_20_3980_mRNA   221 221 4e-144
LinJ_35_5440_mRNA   LbrM_34_0010_mRNA   167 114 4e-66
LinJ_35_5440_mRNA   LbrM_34_0040_mRNA   167 114 4e-65
LinJ_35_5450_mRNA   LbrM_34_0010_mRNA   508 455 0.0
LinJ_35_5450_mRNA   LbrM_34_0040_mRNA   508 424 0.0
LinJ_35_5460_mRNA   LbrM_34_1480_mRNA   296 293 0.0
LinJ_35_5460_mRNA   LbrM_16_0970_mRNA   296 205 3e-25
LinJ_03_0970_mRNA   LbrM_35_6200_mRNA   620 220 2e-23
LinJ_03_0970_mRNA   LbrM_18_0900_mRNA   620 149 2e-05
LinJ_08_1320_mRNA   LbrM_10_1520_mRNA   202 199 3e-62
LinJ_08_1320_mRNA   LbrM_08_0990_mRNA   202 181 3e-61
LinJ_08_1330_mRNA   LbrM_08_0990_mRNA   201 176 5e-60
LinJ_08_1330_mRNA   LbrM_08_1140_mRNA   201 199 2e-58
LinJ_31_3360_mRNA   LbrM_03_0750_mRNA   799 819 0.0
LinJ_31_3360_mRNA   LbrM_34_0520_mRNA   799 226 6e-04
LinJ_31_3370_mRNA   LbrM_03_0740_mRNA   396 342 0.0
LinJ_31_3370_mRNA   LbrM_34_4320_mRNA   396 170 7e-04
LinJ_14_1600_mRNA   LbrM_14_1120_mRNA   859 939 0.0
LinJ_14_1600_mRNA   LbrM_14_1120_mRNA   859 939 0.0
LinJ_14_1600_mRNA   LbrM_14_1120_mRNA   859 946 0.0

Answer 1

[ori]

First, it is necessary to clarify the definition of “60% of conservancy”
(e.g. 60% similarity across 90% of the protein sequence).

Next, try BLASTP with additional -outfmt options, “pident” and “qcovs”.

You will get results with pident (% of identical matches) and qcovs (query coverage per subject) column.
If you set -max_target_seqs 2, you will be able to open the output file in EXCEL and filter your results by their column (e.g. pident>=0.6, qcovs>=0.9).