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

NucPred

Fetching Q07864 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGF    50
  51  ERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPY   100
 101  KPYFYIATRKGCEREVSSFLSKKFQGKIAKVETVPKEDLDLPNHLVGLKR   150
 151  NYIRLSFHTVEDLVKVRKEISPAVKKNREQDHASDAYTALLSSVLQRGGV   200
 201  ITDEEETSKKIADQLDNIVDMREYDVPYHIRLSIDLKIHVAHWYNVRYRG   250
 251  NAFPVEITRRDDLVERPDPVVLAFDIETTKLPLKFPDAETDQIMMISYMI   300
 301  DGQGYLITNREIVSEDIEDFEFTPKPEYEGPFCVFNEPDEAHLIQRWFEH   350
 351  VQETKPTIMVTYNGDFFDWPFVEARAAVHGLSMQQEIGFQKDSQGEYKAP   400
 401  QCIHMDCLRWVKRDSYLPVGSHNLKAAAKAKLGYDPVELDPEDMCRMATE   450
 451  QPQTLATYSVSDAVATYYLYMKYVHPFIFALCTIIPMEPDEVLRKGSGTL   500
 501  CEALLMVQAFHANIIFPNKQEQEFNKLTDDGHVLDSETYVGGHVEALESG   550
 551  VFRSDIPCRFRMNPAAFDFLLQRVEKTLRHALEEEEKVPVEQVTNFEEVC   600
 601  DEIKSKLASLKDVPSRIECPLIYHLDVGAMYPNIILTNRLQPSAMVDEAT   650
 651  CAACDFNKPGANCQRKMAWQWRGEFMPASRSEYHRIQHQLESEKFPPLFP   700
 701  EGPARAFHELSREEQAKYEKRRLADYCRKAYKKIHITKVEERLTTICQRE   750
 751  NSFYVDTVRAFRDRRYEFKGLHKVWKKKLSAAVEVGDAAEVKRCKNMEVL   800
 801  YDSLQLAHKCILNSFYGYVMRKGARWYSMEMAGIVCFTGANIITQARELI   850
 851  EQIGRPLELDTDGIWCVLPNSFPENFVFKTTNVKKPKVTISYPGAMLNIM   900
 901  VKEGFTNDQYQELAEPSSLTYVTRSENSIFFEVDGPYLAMILPASKEEGK   950
 951  KLKKRYAVFNEDGSLAELKGFEVKRRGELQLIKIFQSSVFEAFLKGSTLE  1000
1001  EVYGSVAKVADYWLDVLYSKAANMPDSELFELISENRSMSRKLEDYGEQK  1050
1051  STSISTAKRLAEFLGDQMVKDAGLSCRYIISRKPEGSPVTERAIPLAIFQ  1100
1101  AEPTVRKHFLRKWLKSSSLQDFDIRAILDWDYYIERLGSAIQKIITIPAA  1150
1151  LQQVKNPVPRVKHPDWLHKKLLEKNDVYKQKKISELFTLEGRRQVTMAEA  1200
1201  SEDSPRPSAPDMEDFGLVKLPHPAAPVTVKRKRVLWESQEESQDLTPTVP  1250
1251  WQEILGQPPALGTSQEEWLVWLRFHKKKWQLQARQRLARRKRQRLESAEG  1300
1301  VLRPGAIRDGPATGLGSFLRRTARSILDLPWQIVQISETSQAGLFRLWAL  1350
1351  VGSDLHCIRLSIPRVFYVNQRVAKAEEGASYRKVNRVLPRSNMVYNLYEY  1400
1401  SVPEDMYQEHINEINAELSAPDIEGVYETQVPLLFRALVHLGCVCVVNKQ  1450
1451  LVRHLSGWEAETFALEHLEMRSLAQFSYLEPGSIRHIYLYHHAQAHKALF  1500
1501  GIFIPSQRRASVFVLDTVRSNQMPSLGALYSAEHGLLLEKVGPELLPPPK  1550
1551  HTFEVRAETDLKTICRAIQRFLLAYKEERRGPTLIAVQSSWELKRLASEI  1600
1601  PVLEEFPLVPICVADKINYGVLDWQRHGARRMIRHYLNLDTCLSQAFEMS  1650
1651  RYFHIPIGNLPEDISTFGSDLFFARHLQRHNHLLWLSPTARPDLGGKEAD  1700
1701  DNCLVMEFDDQATVEINSSGCYSTVCVELDLQNLAVNTILQSHHVNDMEG  1750
1751  ADSMGISFDVIQQASLEDMITGGQAASAPASYDETALCSNTFRILKSMVV  1800
1801  GWVKEITQYHNIYADNQVMHFYRWLRSPSSLLHDPALHRTLHNMMKKLFL  1850
1851  QLIAEFKRLGSSVIYANFNRIILCTKKRRVEDAIAYVEYITSSIHSKETF  1900
1901  HSLTISFSRCWEFLLWMDPSNYGGIKGKVSSRIHCGLQDSQKAGGAEDEQ  1950
1951  ENEDDEEERDGEEEEEAEESNVEDLLENNWNILQFLPQAASCQNYFLMIV  2000
2001  SAYIVAVYHCMKDGLRRSAPGSTPVRRRGASQLSQEAEGAVGALPGMITF  2050
2051  SQDYVANELTQSFFTITQKIQKKVTGSRNSTELSEMFPVLPGSHLLLNNP  2100
2101  ALEFIKYVCKVLSLDTNITNQVNKLNRDLLRLVDVGEFSEEAQFRDPCRS  2150
2151  YVLPEVICRSCNFCRDLDLCKDSSFSEDGAVLPQWLCSNCQAPYDSSAIE  2200
2201  MTLVEVLQKKLMAFTLQDLVCLKCRGVKETSMPVYCSCAGDFALTIHTQV  2250
2251  FMEQIGIFRNIAQHYGMSYLLETLEWLLQKNPQLGH                2286

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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