this two proteins are same one?

Question

[john_well]

Hello,

Here, the two proteins are the same one recorded in protein DB at ncbi?

http://www.ncbi.nlm.nih.gov/protein/224028257,693842

1. Accession:NP_001138884.1 GI:224028257
2. Accession: AAB32188.1 GI: 693842

I aligned this two ones and noticed that there are two positions are different, but it seems they should be the same one.

Can somebody help me explain it? and which one should be right or both right?

Thanks

[Sam]

One of them are the refseq gene Nrf2 and the other is by GeneBank. Most likely they are isoform of the same gene as the first one explicitly said that it is isoform 2 of Nrf2.

You can have a detail information here:

http://www.uniprot.org/uniprot/Q16236

[john_well]

Thanks Sam. I have check the uniprot and there are 3 isoform but the isoform-2 is same to GI:224028257, why there is still GI: 693842? they are not duplicated?

Answer 1

[Neilfws]

I think the clue is in the description for the first sequence:

nuclear factor erythroid 2-related factor 2 isoform 2 [Homo sapiens]

So it is an isoform - a slightly-different version of the Nrf2 protein. As you discovered, it differs at 2 positions and so warrants a separate database entry.

No reason why they "should" be the same, nor is one/both "right" in any sense.

[john_well]

Thanks for your response.

One more question is: if I want to use the protein to docking analysis (such as molecular docking or others), which one I should select?

In addition, in the uniprot (http://www.uniprot.org/uniprot/Q16236#sequences), the protein Nuclear factor erythroid 2-related factor 2 has been reported with 3 isoforms and the isoform-2 has 589 amino acids which is same to GI: 224028257 from refseq. So the one from gene bank (GI: 693842) is another isoform of Nuclear factor erythroid 2-related factor 2, which did not reported in uniprot?

Thanks.

Answer 2

[Elisabeth Gasteiger]

UniProtKB entry http://www.uniprot.org/uniprot/Q16236 is mapped to 3 RefSeq identifiers as follows:

NP_001138884.1. NM_001145412.2. [Q16236-2] gi:224028257
NP_001138885.1. NM_001145413.2. [Q16236-3] gi:224028259
NP_006155.2. NM_006164.4. [Q16236-1] gi:20149576

gi number http://www.ncbi.nlm.nih.gov/protein/693842 corresponds to GenBank entry AAB32188 which is also cross-referenced in http://www.uniprot.org/uniprot/Q16236

According to the cross-reference section of this entry, http://www.uniprot.org/uniprot/Q16236#cross_references, AAB32188 presents a different initiation site:

S74017 mRNA. Translation: AAB32188.1. Different initiation.

(see also: http://www.uniprot.org/help/canonical_nucleotide)