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

NucPred

Fetching O15438 from www.uniprot.org...

The NucPred score for your sequence is 0.20 (see score help below)

   1  MDALCGSGELGSKFWDSNLSVHTENPDLTPCFQNSLLAWVPCIYLWVALP    50
  51  CYLLYLRHHCRGYIILSHLSKLKMVLGVLLWCVSWADLFYSFHGLVHGRA   100
 101  PAPVFFVTPLVVGVTMLLATLLIQYERLQGVQSSGVLIIFWFLCVVCAIV   150
 151  PFRSKILLAKAEGEISDPFRFTTFYIHFALVLSALILACFREKPPFFSAK   200
 201  NVDPNPYPETSAGFLSRLFFWWFTKMAIYGYRHPLEEKDLWSLKEEDRSQ   250
 251  MVVQQLLEAWRKQEKQTARHKASAAPGKNASGEDEVLLGARPRPRKPSFL   300
 301  KALLATFGSSFLISACFKLIQDLLSFINPQLLSILIRFISNPMAPSWWGF   350
 351  LVAGLMFLCSMMQSLILQHYYHYIFVTGVKFRTGIMGVIYRKALVITNSV   400
 401  KRASTVGEIVNLMSVDAQRFMDLAPFLNLLWSAPLQIILAIYFLWQNLGP   450
 451  SVLAGVAFMVLLIPLNGAVAVKMRAFQVKQMKLKDSRIKLMSEILNGIKV   500
 501  LKLYAWEPSFLKQVEGIRQGELQLLRTAAYLHTTTTFTWMCSPFLVTLIT   550
 551  LWVYVYVDPNNVLDAEKAFVSVSLFNILRLPLNMLPQLISNLTQASVSLK   600
 601  RIQQFLSQEELDPQSVERKTISPGYAITIHSGTFTWAQDLPPTLHSLDIQ   650
 651  VPKGALVAVVGPVGCGKSSLVSALLGEMEKLEGKVHMKGSVAYVPQQAWI   700
 701  QNCTLQENVLFGKALNPKRYQQTLEACALLADLEMLPGGDQTEIGEKGIN   750
 751  LSGGQRQRVSLARAVYSDADIFLLDDPLSAVDSHVAKHIFDHVIGPEGVL   800
 801  AGKTRVLVTHGISFLPQTDFIIVLADGQVSEMGPYPALLQRNGSFANFLC   850
 851  NYAPDEDQGHLEDSWTALEGAEDKEALLIEDTLSNHTDLTDNDPVTYVVQ   900
 901  KQFMRQLSALSSDGEGQGRPVPRRHLGPSEKVQVTEAKADGALTQEEKAA   950
 951  IGTVELSVFWDYAKAVGLCTTLAICLLYVGQSAAAIGANVWLSAWTNDAM  1000
1001  ADSRQNNTSLRLGVYAALGILQGFLVMLAAMAMAAGGIQAARVLHQALLH  1050
1051  NKIRSPQSFFDTTPSGRILNCFSKDIYVVDEVLAPVILMLLNSFFNAIST  1100
1101  LVVIMASTPLFTVVILPLAVLYTLVQRFYAATSRQLKRLESVSRSPIYSH  1150
1151  FSETVTGASVIRAYNRSRDFEIISDTKVDANQRSCYPYIISNRWLSIGVE  1200
1201  FVGNCVVLFAALFAVIGRSSLNPGLVGLSVSYSLQVTFALNWMIRMMSDL  1250
1251  ESNIVAVERVKEYSKTETEAPWVVEGSRPPEGWPPRGEVEFRNYSVRYRP  1300
1301  GLDLVLRDLSLHVHGGEKVGIVGRTGAGKSSMTLCLFRILEAAKGEIRID  1350
1351  GLNVADIGLHDLRSQLTIIPQDPILFSGTLRMNLDPFGSYSEEDIWWALE  1400
1401  LSHLHTFVSSQPAGLDFQCSEGGENLSVGQRQLVCLARALLRKSRILVLD  1450
1451  EATAAIDLETDNLIQATIRTQFDTCTVLTIAHRLNTIMDYTRVLVLDKGV  1500
1501  VAEFDSPANLIAARGIFYGMARDAGLA                         1527

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.)

Go back to the NucPred Home Page.