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

NucPred

Fetching O55207 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MALSKGLRLLARLDPTGPSSVLLEARGRGDCLLFEAGAVATLAPEEKEVI    50
  51  KGLYGKPTDAYGCLGELSLKSGGVPLSFLVLVTGCTSVGRIPDAEIYKIT   100
 101  GTEFYPLQEEAKEEDRLPALKKILSSGVFYFAWPNDGACFDLTIRAQKQG   150
 151  DDCSEWGTSFFWNQLLHVPLRQHQVNCHDWLLKVICGVVTIRTVYASHKQ   200
 201  AKACLISRISCERAGARFLTRGVNDDGHVSNFVETEQAIYMDDGVSSFVQ   250
 251  IRGSVPLFWEQPGLQVGSHHLRLHRGLEANAPAFERHMVLLKEQYGQQVV   300
 301  VNLLGSRGGEEVLNRAFKKLLWASCHAGDTPMINFDFHQFAKGRKLEKLE   350
 351  NLLRPQLKLHWDDFGVFAKGENVSPRFQKGTLRMNCLDCLDRTNTVQCFI   400
 401  ALEVLHLQLESLGLNSKPITDRFVESFKAMWSLNGHGLSKVFTGSRALEG   450
 451  KAKVGKLKDGARSMSRTIQSNFFDGVKQEAIKLLLVGDVYNEESTDKGRM   500
 501  LLDNTALLGLGSNKQNSLSGMLDGKATPRILKAMTERQSEFTNFKRIQIA   550
 551  MGTWNVNGGKQFRSNLLGTTELTDWLLDAPQLSGAVDSQDDGGPADIFAV   600
 601  GFEEMVELSAGNIVNASTTNRKMWGEQLQKAISRSHRYILLTSAQLVGVC   650
 651  LYIFVRPYHVPFIRDVAIDTVKTGMGGKAGNKGAVGIRFQFHSTSFCFIC   700
 701  SHLTAGQSQVKERNEDYREITHKLSFPSGRNIFSHDYVFWCGDFNYRIDL   750
 751  TYEEVFYFVKRQDWKKLMEFDQLQLQKSSGKIFKDFHEGTINFGPTYKYD   800
 801  VGSAAYDTSDKCRTPAWTDRVLWWRKKHPYDKTAGELNLLDSDLDGDANI   850
 851  RHTWSPGTLKYYGRAELQASDHRPVLAIVEVEVQEVDVGARERVFQEVSS   900
 901  VQGPLDATVIVNLQSPTLEERNEFPEDLRTELMQTLGNYGTIILVRINQG   950
 951  QMLVTFADSHSALSVLDVDGMKVKGRAVKIRPKTKDWLEGLREELIRKRD  1000
1001  SMAPVSPTANSCLLEENFDFTSLDYESEGDVLEDDEDYLADEFGQPVVSD  1050
1051  SELGGDDSSDTMSASTPASKSPALAKKKQHPTYKDDADLMTLKLELEVAG  1100
1101  NFRHRSPSRSLSVPNRPRPPHPPQRPPPPTGLMVKKSASDASISSGTHGQ  1150
1151  YSILQTAKLLPGAPQQPPKARTGISKPYNVKQIKTTNAQEAEAAIRCLLE  1200
1201  AGGGVPESAPGATPLRNQGSSKPEASLGPPVLPRRPVPRVPTMKKPTLRR  1250
1251  TGKPMLPEEQCEQQPVHFTMASQEMNLETPPPITAPIPPVPKPRTFQPGR  1300
1301  GVERRPSGGKPEPDDAPPVTGAVELSSPEAPEAPSLAPKVPPRRKKSAPA  1350
1351  AFHLQVLQSNSQLLQGLTCSSSSPSPPKPDTPLLYPQMALGTSSAISPET  1400
1401  DGPRVTEPEAASFHGDYPDPFWSLLHHPKLLNNNTWLSKSSEPLDLGSRT  1450
1451  PERTHTDSAQVNASVVERGLPPDHGGKDFSHWMAASNKDKRTTLGV      1496

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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