SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9WVF7 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MVLRNSGRRHPEPGADGEGSRDDGPSSSVSALKRLERSQWTDKMDLRFGF    50
  51  ERLKEPGERTGWLINMHPTEILDEDKRLVSAVDYYFIQDDGSRFKVALPY   100
 101  MPYFYIAARKGCDREVSSFLSKKFQGKIAKLENVPKEDLDLPNHLVGLKR   150
 151  SYIKLSFHTVEDLVKVRKEISPAVKKNREQDHASDEYTTMLSSILQGGSV   200
 201  ITDEDETSKKIADQLDNIVDMREYDVPYHIRLSIDLRIHVAHWYNVRFRG   250
 251  NAFPVEITRRDDLVERPDPVVLAFDIETTKLPLKFPDAETDQIMMISYMI   300
 301  DGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDEVHLIQRWFEH   350
 351  IQETKPTIMVTYNGDFFDWPFVEARAAIHGLSMYQEIGFQKDSQGEYKAP   400
 401  QCIHMDCLRWVKRDSYLPVGSHNLKAAAKAKLGYDPVELDPEDMCRMATE   450
 451  QPQTLATYSVSDAVATYYLYMKYVHPFIFALCTIIPMEPDEVLRKGSGTL   500
 501  CEALLMVQAFHANIIFPNKQEQEFNKLTDDGHMLDAETYVGGHVEALESG   550
 551  VFRSDIPCRFRMNPAAFDFLLQRVEKTMRHAIEEEEKVPVEQATNFQEVC   600
 601  EQIKTKLTSLKDVPNRIECPLIYHLDVGAMYPNIILTNRLQPSAIVDEAT   650
 651  CAACDFNKPGASCQRKMAWQWRGEFMPASRSEYHRIQHQLESEKFPPLFP   700
 701  EGPARAFHELSREEQAKYEKRRLADYCRKAYKKIHVTKVEERLTTICQRE   750
 751  NSFYVDTVRAFRDRRYEFKGLHKVWKKKLSAAVEVGDASEVKRCKNMEIL   800
 801  YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELI   850
 851  EQIGRPLELDTDGIWCVLPNSFPENFVIKTTNAKKPKLTISYPGAMLNIM   900
 901  VKEGFTNHQYQELTEPSSLTYVTHSENSIFFEVDGPYLAMILPASKEEGK   950
 951  KLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLE  1000
1001  EVYGSVAKVADYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQK  1050
1051  STSISTAKRLAEFLGDQMVKDAGLSCRYIISRKPEGSPVTERAIPLAIFQ  1100
1101  AEPTVRKHFLRKWLKSSSLQDFDIRTILDWDYYIERLGSAIQKIITIPAA  1150
1151  LQQVKNPVPRVKHPDWLHKKLLEKNDIYKQKKISELFVLEGKRQIVMAQA  1200
1201  SENSLSLCTPDMEDIGLTKPHHSTVPVATKRKRVWETQKESQDIALTVPW  1250
1251  QEVLGQPPSLGTTQEEWLVWLQFHKKKWQLQAQQRLALRKKQRLESAEDM  1300
1301  PRLGPIREGPSTGLGSFLRRTARSIMDLPWQIIQISETRQAGLFRLWAII  1350
1351  GNDLHCIKLSIPRVFYVNQRVAKAEDGPAYRKVNRALPRSNIVYNLYEYS  1400
1401  VPEDMYQEHINEINTELSVPDIEGVYETQVPLLFRALVQLGCVCVVNKQL  1450
1451  TRHLSGWEAETFALEHLEMRSLAQFSYLEPGSIRHIYLYHHTQGHKALFG  1500
1501  VFIPSQRRASVFVLDTVRSNQMPGLSALYSSEHSLLLDKVDPKLLPPPKH  1550
1551  TFEVRAETNLKTICRAIQRFLLAYKEERRGPTLIAVQSSWELCRLTSEIP  1600
1601  VLEEFPLVPIRVADKISYAVLDWQRHGARRMIRHYLNLDLCLSQAFEMSR  1650
1651  YFHIPVGNLPEDISTFGSDLFFARHLQHHNHLLWLSPTSRPDLGGKEADD  1700
1701  NRLVMEFDDRATVEINSSGCYSTVCVELDIQNLAVNTILQSHHVNDMEGA  1750
1751  GSMGISFDVIQQASLEDMVTGNQAASALANYDETALCSSTFRILKSMVVG  1800
1801  WVKEITQYHNIYADNQVMHFYRWLQSPCSLLHDPALHRTLHNMMKKLFLQ  1850
1851  LIAEFKRLGSSVVYANFNRIILCTKKRRIEDALAYVEYITNSIHSKEIFH  1900
1901  SLTISFSRCWEFLLWMDPSNYGGIKGKVPSSIHCGQVKEQDSQAREETDE  1950
1951  EEEDKEKDEEEEGMGESEVEDLLENNWNILQFLPQAASCQSYFLMIVSAY  2000
2001  IVAVYQSMKEELRHSAPGSTPVKRKGASQFSQESEGATGSLPGMITFSQD  2050
2051  YVANELTQSFFTITQKIQKKVTGSRNTTEPSEMFPVLPGSHLLLNNPALE  2100
2101  FIKYVCKVLSLDTNITNQVNKLNRDLLRLVDVGEFSEEAQFRDPCHSYVL  2150
2151  PEVICHSCNFCRDLDLCKDSSFSQDGAILPQWLCSNCQAPYDSSAIESAL  2200
2201  VEALQRKLMAFTLQDLVCLKCRGMKETHMPVYCSCAGDFTLTIRTEVFME  2250
2251  QIRIFQNIAKYYSMSYLQETIEWLLQTSPVSNC                   2283

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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