Question about potentially mutation causing protein

Question

[M K]

Is the following chunk of protein sequence, cause any mutation. I didn't find enough information about this protein. I know it easy to search for it using available database, but the issue here I didn't find source with full details.

GEMVTKAKCKFCYKLYVYQPGGPTSQLNRHLDKCTAYQNKLANAKSKVAQGTISFALDDGSLVVNPTEYD LDMEDDFSLSLSSEDGGSQGEDEVHNAKRGVKRAKGDVPLSPSKCKVKRVKRADCWKYFKVVEVQSKKKF GEMVTKAKCKFCYKLYVKRAKGDVPLSPSKCKVKRVKRADCWKYFKVVEVISFALDDGSLVVNPTEYD HDHTRNLIAKMIIVHEYSLRMVEHRWFNILMKWMNN

[Medhat]

what was the result of aligning this protein against the database?

maybe it is uncharacterized protein of maize or rice?

[M K]

I used blastp, and it gave me long matching

this is the first one with the following information 236 236 78% 1e-73 59% CAE75980.1 wich is : B1160F02.11 [Oryza sativa Japonica Group] GenBank: CAE75980.1

the second one 243 243 85% 3e-72 58% BAF04701.2 the third one 182 182 78% 7e-50 47% XP_015624332.1 I don't know which one will be the accurate one regarding the coverage %. Also there are 4 others befor those in the blast list and the first one is uncharacterized and the other 3 are hypotheticals

[GenoMax]

How are we supposed to help you with a protein that you do not seem to know much about either :)

[Eric Lim]

Have you tried blat'ing the sequence using the UCSC BLAT search?

http://genome.ucsc.edu/cgi-bin/hgBlat

[GenoMax]

That appears to be a plant sequences based on a couple of posts above.

[M K]

So the question here what is the specific name of this protein. if the named or accession number is known it will be easy to look for more details about it

[GenoMax]

No offense but this is not an exercise/homework question, correct?

[M K]

No it is not. I am just curious about it. what I found so far it is uncharacterized corn protien

[GenoMax]

Try Blast search over at Uniprot.org. Appears to be a plant (rice) protein.

[M K]

Do you mean for Japanese rice

[GenoMax]

Oryza genus at least (which will include rice). Based on the hits you only appear to have a fragment of the total protein (~40%).

Why do you expect this to be mutagenic and to which organism?

[M K]

Based on the domain for it which include Zinc finger which play a role for binding DNA, I expect may cause mutation, but so far I don't know what is it.

[Eric Lim]

Yeah. For whatever reason, I just assume every protein in the universe is human. Need my caffeine fix.

Answer 1

[Michael]

Using NCBI Blastp we find the best match as given below, 100% seq identity, full query coverage, only the first 10 AA missing. The next best hit is not as good. So I guess it is reasonable to assume that this sequence "is" from Corn XP_008680584.1

You can read more about the BED Zinc finger domain here: http://www.ebi.ac.uk/interpro/entry/IPR003656 The main biological function of Zinc finger domains is to bind DNA, this could be a regulatory protein, transcription factor, or transposase, and there you also have your potential for mutagenesis.

PREDICTED: uncharacterized protein LOC103655641 [Zea mays]
Sequence ID: XP_008680584.1Length: 257Number of Matches: 1
Related Information
Gene-associated gene details
Map Viewer-aligned genomic context
Range 1: 11 to 257GenPeptGraphicsNext MatchPrevious Match
Alignment statistics for match #1
Score   Expect  Method  Identities  Positives   Gaps
518 bits(1334)  0.0 Compositional matrix adjust.    247/247(100%)   247/247(100%)   0/247(0%)
Query  1    SLGSRSRTRTKQLTKKPPISMQKMHATTASSASGNRSNVSISVEPTTNSREEEDKDEDNS  60
            SLGSRSRTRTKQLTKKPPISMQKMHATTASSASGNRSNVSISVEPTTNSREEEDKDEDNS
Sbjct  11   SLGSRSRTRTKQLTKKPPISMQKMHATTASSASGNRSNVSISVEPTTNSREEEDKDEDNS  70

Query  61   LDMEDDFSLSLSSEDGGSQGEDEVHNAKRGVKRAKGDVPLSPSKCKVKRVKRADCWKYFK  120
            LDMEDDFSLSLSSEDGGSQGEDEVHNAKRGVKRAKGDVPLSPSKCKVKRVKRADCWKYFK
Sbjct  71   LDMEDDFSLSLSSEDGGSQGEDEVHNAKRGVKRAKGDVPLSPSKCKVKRVKRADCWKYFK  130

Query  121  VVEVQSKKKFGEMVTKAKCKFCYKLYVYQPGGPTSQLNRHLDKCTAYQNKLANAKSKVAQ  180
            VVEVQSKKKFGEMVTKAKCKFCYKLYVYQPGGPTSQLNRHLDKCTAYQNKLANAKSKVAQ
Sbjct  131  VVEVQSKKKFGEMVTKAKCKFCYKLYVYQPGGPTSQLNRHLDKCTAYQNKLANAKSKVAQ  190

Query  181  GTISFALDDGSLVVNPTEYDHDHTRNLIAKMIIVHEYSLRMVEHRWFNILMKWMNNSYES  240
            GTISFALDDGSLVVNPTEYDHDHTRNLIAKMIIVHEYSLRMVEHRWFNILMKWMNNSYES
Sbjct  191  GTISFALDDGSLVVNPTEYDHDHTRNLIAKMIIVHEYSLRMVEHRWFNILMKWMNNSYES  250

Query  241  IGRKTKK  247
            IGRKTKK
Sbjct  251  IGRKTKK  257

[GenoMax]

Interesting you find something other than what OP did (your blast flavor/choice of DB must be different). This is a predicted protein based on the genome sequence, so if it is real would need experimental investigation.

[Michael]

I simply pasted the sequence into NCBI blast, not sure what can go wrong with that. Maybe op used local blast with a custom db.

[Eric Lim]

Also there are 4 others befor those in the blast list and the first one is uncharacterized and the other 3 are hypotheticals

I thought the OP did. I also got this uncharacterized protein using default param and db, but didn't respond with the assumption that OP found it and wasn't interested.