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

NucPred

Fetching Q09716 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MKALDIDTILTQISNQQSLDKRYKRIKRLINNEQFCKNVILQKLVDSTKD    50
  51  IIENKVHGNILAATISLWTHAAEKHKEMSSDDRALLFNELSKVPNSEYYP   100
 101  ATVDALIVITSQGERTESFSNDILKVLSEWLTDLFTIIDDMRAQSRKSFK   150
 151  GSAELRNYTRCFRQIILLLTNMFRVGFNLFDEMEVSSMLANCVWVSKSTT   200
 201  DEEDIALVFSLLNCIISYGRISSAVLYSIVEVVCRAKFGLVASSQSAQQI   250
 251  VEKLLKTATKYEALNSLKRIMEETDEGSYIAIMGGIQIVSALFTDIPRSV   300
 301  YCTRGMLLGFLQRSLKNKSSRIALETTRSLYNALERRSFVEVLYADEWIS   350
 351  LLDLLVEISSSLPKSLNYRPGTWQHIEPNIIESIASYQLQHLLLFNEILK   400
 401  PDSNHFVLEKFHEFLKINFSYLTPTLSQKLFTVLDLRSQLPYSEGWLEDQ   450
 451  TILLKSYFDTSFSLDFHVYLIGLFRKVLFACPVELRPEVYARMLCPLVKS   500
 501  LDKSSSEVIIDEVISLVCDLSWIYPSNVFHEVKDSLCFYAHNSSNGDLQL   550
 551  RSIQAIVSLTFYYVLLPEFKSVLYDGLVEISCDFKIRRTFRIPVLKLLLQ   600
 601  LRINTNDYCFVNLSPAQLELISVYSTQWHNPFISEEAQRCRDNKVKDRDL   650
 651  SFSPVFQKFPLKVNTSATLSKDLMSLPINEWVKNVMYIVTHETDWKVVQY   700
 701  ILINFTNQLRNTKMFTKTVEALQLLLNSLRDIINGKQSLNINFSDFFRIE   750
 751  DLLVSLSKILSVLMVYKDVLPPTAHEQFFQLLNRFAEKGDKTMESCIDTL   800
 801  ITNCCAMQSFSIMHLPKFFSITMSSNLSERSLVNFLRLLHVVSDNWELNE   850
 851  GLEKETIQSICLFCLKVIRTKKEELDGHKKLVNPNTKVFCLYLVSFSYSI   900
 901  ISNLFLGCETTERAQLASFLLKEFLNLKNGSHFEGYERVFYELLLRYTYS   950
 951  DERIESYPSDSRFHFNSSSKSWLYRGCVITINAEYETGDYQMILRRMSGT  1000
1001  TIYRFWRNMRDRGAFEKSLMMEQSMVSSELKQKYLQEIAASHVFMETVLS  1050
1051  PLDSPDEEPILIKPDARTEELIQSLDATHTKPVINIAVALQAGDVSDINT  1100
1101  TVGWQLFYRLLESFGHEKKLDNGETIYVWQSKTIEMIFRYVSDPAEALES  1150
1151  SLYSSLIIIGSDDLVGPDSLNWDSVDVPVIIKISLDSHLDALKMFDTLFH  1200
1201  VKLEIITTGTDISHQSFWKLDQIISTNSIAPLLHSYLADIGLYQMIFENF  1250
1251  AYVHPWLLRQQYIDTLYTIHQVPTTQRESSALPSDKTFDFTLFL        1294

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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