Amino Acid - Unknown Symbol

Question

[Allen Alger]

The following amino acid sequence was published in a research paper I'm studying. The sequence contains a ")" about 3/4 of the way into the sequence. What does this ")" mean?

This is what it looks like: The ")" is in the next to the last line.

1 SUMO3-11Arg PTD – SODMLS - MatureTFAM
MGHHHHHHGGMSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLS
MRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGRRRRRRRRRRRGEGDIMG
EWGNEIFGAI AGFLGGE MLSRAVCGTSR QLPPVLGYLGSRQ SSVLASCPKKPVSSYLR
FSKEQLPIFK AQNPDAKTTELIRRIAQRWR ELPDSKKKIYQDAYRAEWQVYKEEISRFKE
QLTPSQIM SLEKEIMD KHLKRKAM TKKKELTLLGKPKRPRSAYN VYVAERFQEA
KGDSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETRYHN EMKSWEEQ MIEVGRKD
LLRRTIKKQR KYGAEEC) KGDSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETRYHN
EMKSWEEQ MIEVGRKD LLRRTIKKQR KYGAEEC

Allen

[Egon Willighagen]

Please contact the authors, ask them what it is about, and let us know the answer here!

Answer 1

[Neilfws]

Unless the authors have defined the symbol elsewhere in the paper, it means that the journal editors are not very good at proof-reading. The ")" has no standard meaning in this context and may be a typographical error.

EDIT: Having looked at the paper (this one I assume?), I see the authors have used all kinds of odd notation in describing the sequence. However, the ")" symbol still seems oddly out of place.

Answer 2

[Woa]

This stretch of sequence 'KGDSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETRYHN EMKSWEEQ MIEVGRKD LLRRTIKKQR KYGAEEC' occurs before and after the parentheses ")" symbol and could be just a printing error. Blast the protein (omitting the parentheses) against Uniprot and you'll see the first hit contains no such repeat.

[Woa]

After reading the literature it looks like that it is a chimeric protein sequence made of some fused domains/linkers. So, the ')' seems to mark some domain boundary.

Answer 3

[Joseph Hughes]

A quick protein blast of the sequence shows that beyond the bracket, the blast score is below 200. This is probably the result of some sort of typo as the last 160 aa are in fact a repeat:

KGDSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETRYHN EMKSWEEQ MIEVGRKD LLRRTIKKQR KYGAEEC)

KGDSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETRYHN EMKSWEEQ MIEVGRKD LLRRTIKKQR KYGAEEC

When looking at the full length coding sequence of the top blast match there is no such repeat:

MAFLRSMWGVLTALGRSGAELCTGCGSRLRSPFSFAYLPRWFSSVLASCPKKPVSSYLRFSKEQLPIFKA QNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKR KAMTKKKELTLLGKPKRPRSAYNVYVAERFQEA KGDSPQEKLK TVKENWKNLS DSEKELYIQH AKEDETR YHN EMKSWEEQ MIEVGRKD LLRRTIKKQR KYGAEEC