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

NucPred

Fetching P34367 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MKAIIHDDTVVREIEGQRVQVLQKFADFELKAINKRSSIIQSRQLQVYLR    50
  51  SAAEFKQVIESLIESSEAVVTSQCSESSIRGQKVIGRLQQEADGKHNNLP   100
 101  MLENEAARLLKEGHYASDEIQKTFNNVLSRWEYLLKLLALKWRQLEKEIE   150
 151  SIEFKNKCDSIVDWILKIKESDESGKEIFDEIRKCSMVWNEISATFQQML   200
 201  DPTATDTSNYEKVHETWSNFQEYIDSLHKKLSENERFQKFVDNAEDLIKW   250
 251  MDDKEKEICEKYSKMDFEVMMKYRKTVEIEMKSVEQRIKDLKEQFVGMEN   300
 301  DNLRNIPDPKNHVIDVEQRFESFQAFVQKWKTDIENSADADKLMKEAENI   350
 351  CCWSSEKIEDLKIMATSDTPDCDEIIMWIETNNFDFNSWDNVVVQFLASS   400
 401  QELLNKQNNGNVKQEVERTTELYELAKRTMKTCNEFLEDRIQTINMEKLI   450
 451  FQTHQKAVILASFLQNHEESPEDMNAEDIEKEIRVIDGITVRCTSVVEQI   500
 501  ENIEDELRQKPEQLNQLSVYASKQVNDLNEMKEVLKTTVNSRKAILQRLL   550
 551  DVTYFLDNCCETRKHTDTMLSNVKSSRVKLEIVQPIKDQLDSLKVEMVDM   600
 601  MLDDQQKNMANEELRKTYENLKKIEMEVGRQASQKEARKAADRTEAFVGR   650
 651  VQNWIDNNQIQDDTDIVSETVNLRRTTTHYQHLLSICASYKKSIDSKLEE   700
 701  LANVYTDNDPRCLLEGIQNSVENFEVKIHQKVDDTKKLLHITENMNELNS   750
 751  QNEWIRAKIKSLSAEPLWDSLLIAQKMRRRHDNDFEEIANRRKQITEVIQ   800
 801  KSATTKDQPILLEIEQNWDRMKDLFDERGGVLERIIKLYEYDEESSTTSE   850
 851  WLREKMICADTIEPKEDESFNEVMVKKLEALTEEVENYKPRIVETHALLE   900
 901  DALVTPNTKDSTSQQTMKLKAVLARKQGEIESDYKALKKLVERKLKTLKA   950
 951  ILQDADISHQIADIEQWIEVEQNQLNRYLASDSDELPTKLDDVMTNIQRR  1000
1001  RSNLTDIKCNVVGQVQMQKIDDAFGMLDVFSFEVHRIRQKACRLEIFKKL  1050
1051  ESQTEDVIDAIQMKLEEINVSQSTSRKRQVAGDDLSNLAGDLETLRRRVV  1100
1101  EALDRSKEVRAANADLAPQVYDTEERLEKQWTDVSKAYENHKKRMERCKI  1150
1151  LSELDNEMINMEQWIDTFNEEVTVVIGSIHDGLGVQVGLESIDTWREELS  1200
1201  HRVDQLGGVKNSLSSVGNAITEQDKMDPWLERVSNIENNLVKARETIDTK  1250
1251  QDDLCRFADILGAERDCERLYSWASGKRHQLETEATMCDAKTLVRRMNEV  1300
1301  EKMMMSRIGEVDQLRDFLDNLKASKTSDTFQTTELENKFELLDVEWNHLE  1350
1351  EELRRREVDLNDSMSQILIDEQFDTIRQWIKERTEALEADVEVSNKTKPD  1400
1401  DIERMQKRHDELASDINDYHTIYEDFLNNGQVEEEKVQVIRHLWSSLIES  1450
1451  STTRQKSLAQECQKSRLFELLDGMSIWLIDAETDVHSTTNFIGLYNSVDA  1500
1501  EKASRLLVSLGEQAGEKDDILIRIQCDESVDVIVEKLRNGISQLQMLIKA  1550
1551  NNEDLDVWKSMQKVVTAIDDEICWFKEINVIFSSTNVGNDVSSNDVLKRK  1600
1601  HQRLQLETQRREQKVAKVVYLTTELVSSHRRPSLEYKFVEIDEKVAELTE  1650
1651  LLESNRQIAEIRTNRLEKWTEYFVTMNEIREKEQLLDQILDLKTGLPETV  1700
1701  LADVERKLQVLETVGDHMDTLTIKAEQMSDDEVIRTKVAVTAIDQLRKKW  1750
1751  LKMNEELKKMHQKIKESIEFTKFVSTCDTGIQCIREQEEKIGNLVRHQKP  1800
1801  ASNFENTAYHSTMTFVETYTKDTFEKLKVVCRKLQNSTDAEKKLSLVSER  1850
1851  LNALKKQLDLLAEKIAVDDKFKLKVQNIQDEYSRTACELGNWLEQAEEDV  1900
1901  SDVVWFQTKDSSEDCRETLLEILGTLRNEKSDLLGELELLEVELAELKED  1950
1951  VKTFTWHSFKTLATRMERLDQTISDRIRIADGEISRHSDNEKICEQAACT  2000
2001  LKTYHNVIVDVKKELEILYSLKLEDQKKSLINLIDKVQKRGMIQDLEKWR  2050
2051  SLMESRYIFNNKFSSATPHGVLVEMCQCLELMSSMLRSVEQSIADRNHNG  2100
2101  VTEKQLHEFELAFDYFDRERNGWLDYKHFELCLKSQGYNFSAENTLKETM  2150
2151  TLLDPSTTGHIQKHDYVRYMVKHETTNILDDHSAIEDALKNLDARKISDS  2200
2201  MPRKEAEFFMSKIAKHAETSSDQVYLEYKDFVNSFY                2236

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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