How to download protein sequences
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5 days ago
Nelo • 0

Hi

I need to download Aquaporin protein fasta sequences of Melon plant species. From the paper it was mentioned that the number of AQP protein in melon is 31 with given Gene ID like 103501427, 103482758, 103491188. If i search in NCBI using this ID, different result popup instead of AQP while in Uniprot, AQP of melon is being displayed.

Is there any way to download all this 31 AQP protein sequences using any tools or NCBI entrez or any other program without using this Gene ID "OR" downloading without the help of accession number ??

Any hints Tnkq

plant fasta AQP • 214 views
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while in Uniprot, AQP of melon is being displayed

So those are UniProt Id's and not NCBI ID's then?

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5 days ago
GenoMax 106k

Using Entrezdirect: (sequences truncated for space, there are a total of 94).

$ esearch -db protein -query "aquaporin AND Cucumis melo [orgn]" | efetch -format fasta 

>NP_001380707.1 aquaporin PIP1-1 [Cucumis melo]
MEGKEEDVRLGANKFNERQPIGTAAQSQDDAKDYKEPPPAPLFEPEELTSWSFYRAGIAEFFATFLFLYI

>NP_001380722.1 aquaporin XIP1-1 [Cucumis melo]
MAQEEFALPLEEEEGRSFDEQTSSSSSFLSRFLIYIGAHELFSQEMWKAAMTELVATALLIFCLTTSIVS

>NP_001380721.1 aquaporin NIP5-2 [Cucumis melo]
MAQFEIVRVDSPKRSQILDVSLTRKVAAEFVGTFILIFGATAAPIVNQKYNSPMSLIGNAACSGIAVMIV

>NP_001380720.1 aquaporin NIP4-1 [Cucumis melo]
MATKIDGIEDEEISKLEEGTVVSAIARLCPSNSVVIIQKVIAELIGTYFVIFSGCGAVAVNKIYGSVTFP
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Thank you so much.

This command is actually retrieving all the AQPs including the isoforms of Melon species. I got 94 sequences, but still it is ok for me. Rest I will manually filter the sequences .

Tnks a lot!!!

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okie

Done

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