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

NucPred

Fetching Q9Y2E4 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MADRSLEGMALPLEVRARLAELELELSEGDITQKGYEKKRSKLIGAYLPQ    50
  51  PPRVDQALPQERRAPVTPSSASRYHRRRSSGSRDERYRSDVHTEAVQAAL   100
 101  AKHKERKMAVPMPSKRRSLVVQTSMDAYTPPDTSSGSEDEGSVQGDSQGT   150
 151  PTSSQGSINMEHWISQAIHGSTTSTTSSSSTQSGGSGAAHRLADVMAQTH   200
 201  IENHSAPPDVTTYTSEHSIQVERPQGSTGSRTAPKYGNAELMETGDGVPV   250
 251  SSRVSAKIQQLVNTLKRPKRPPLREFFVDDFEELLEVQQPDPNQPKPEGA   300
 301  QMLAMRGEQLGVVTNWPPSLEAALQRWGTISPKAPCLTTMDTNGKPLYIL   350
 351  TYGKLWTRSMKVAYSILHKLGTKQEPMVRPGDRVALVFPNNDPAAFMAAF   400
 401  YGCLLAEVVPVPIEVPLTRKDAGSQQIGFLLGSCGVTVALTSDACHKGLP   450
 451  KSPTGEIPQFKGWPKLLWFVTESKHLSKPPRDWFPHIKDANNDTAYIEYK   500
 501  TCKDGSVLGVTVTRTALLTHCQALTQACGYTEAETIVNVLDFKKDVGLWH   550
 551  GILTSVMNMMHVISIPYSLMKVNPLSWIQKVCQYKAKVACVKSRDMHWAL   600
 601  VAHRDQRDINLSSLRMLIVADGANPWSISSCDAFLNVFQSKGLRQEVICP   650
 651  CASSPEALTVAIRRPTDDSNQPPGRGVLSMHGLTYGVIRVDSEEKLSVLT   700
 701  VQDVGLVMPGAIMCSVKPDGVPQLCRTDEIGELCVCAVATGTSYYGLSGM   750
 751  TKNTFEVFPMTSSGAPISEYPFIRTGLLGFVGPGGLVFVVGKMDGLMVVS   800
 801  GRRHNADDIVATALAVEPMKFVYRGRIAVFSVTVLHDERIVIVAEQRPDS   850
 851  TEEDSFQWMSRVLQAIDSIHQVGVYCLALVPANTLPKTPLGGIHLSETKQ   900
 901  LFLEGSLHPCNVLMCPHTCVTNLPKPRQKQPEIGPASVMVGNLVSGKRIA   950
 951  QASGRDLGQIEDNDQARKFLFLSEVLQWRAQTTPDHILYTLLNCRGAIAN  1000
1001  SLTCVQLHKRAEKIAVMLMERGHLQDGDHVALVYPPGIDLIAAFYGCLYA  1050
1051  GCVPITVRPPHPQNIATTLPTVKMIVEVSRSACLMTTQLICKLLRSREAA  1100
1101  AAVDVRTWPLILDTDDLPKKRPAQICKPCNPDTLAYLDFSVSTTGMLAGV  1150
1151  KMSHAATSAFCRSIKLQCELYPSREVAICLDPYCGLGFVLWCLCSVYSGH  1200
1201  QSILIPPSELETNPALWLLAVSQYKVRDTFCSYSVMELCTKGLGSQTESL  1250
1251  KARGLDLSRVRTCVVVAEERPRIALTQSFSKLFKDLGLHPRAVSTSFGCR  1300
1301  VNLAICLQGTSGPDPTTVYVDMRALRHDRVRLVERGSPHSLPLMESGKIL  1350
1351  PGVRIIIANPETKGPLGDSHLGEIWVHSAHNASGYFTIYGDESLQSDHFN  1400
1401  SRLSFGDTQTIWARTGYLGFLRRTELTDANGERHDALYVVGALDEAMELR  1450
1451  GMRYHPIDIETSVIRAHKSVTECAVFTWTNLLVVVVELDGSEQEALDLVP  1500
1501  LVTNVVLEEHYLIVGVVVVVDIGVIPINSRGEKQRMHLRDGFLADQLDPI  1550
1551  YVAYNM                                              1556

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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