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

NucPred

Fetching Q12280 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MTAYSGSPSKPGNNNSYLNRYVENLGTNVTPPLRPQSSSKINSSLNIASP    50
  51  SHLKTKTSASNSSATILSKKVESSVSKLKPSLPNKLVGKYTVDLSNYSKI   100
 101  ELRYYEFLCRVSEVKIWIEAVIEEALPSEIELCVGDSLRNGVFLAKLTQR   150
 151  INPDLTTVIFPAGDKLQFKHTQNINAFFGLVEHVGVPDSFRFELQDLYNK   200
 201  KNIPQVFETLHILISMINKKWPGKTPALTNVSGQISFTKEEIAACKKAWP   250
 251  RIRDFKSLGTNINTAPASPEEPKEKRSGLIKDFNKFERPNIPVEEILITP   300
 301  RKNITDANCSDFSNTPSPYNEAPKMSNLDVVVEKRKFTPIEPSLLGPTPS   350
 351  LEYSPIKNKSLSYYSPTISKYLTYDTEFYTRRSRAREEDLNYYQTFKYSP   400
 401  SHYSPMRRERMTEEQFLEKVVQLQNICRGVNTRFNLYIQKRLLNLFEQDI   450
 451  LRFQACLRGNKFRVLSSMYLPIRRAKIDVPHVEAIQSRIKGSRIRYKYDK   500
 501  LKFTLSRFSCTVELLQAYCRSKLLKTTVNTKLNDIEISHYPLTKLQSYMR   550
 551  ASYVRKKVMSLNTKLNDERESIMKFSAIIRGNVVRCSEDAILSAVHDVHK   600
 601  ENISKLQSLIRGIFTRSCLASIIYSLGKENCNIIQLSACIRGNAVRHKVQ   650
 651  SLFAPENNLSETVHDLQGLVRGILVRYTLDLVDDIVEYNNLALFQAFSRG   700
 701  ALVRESLDQKSSFYKRNVRSVIMIQSWIRKSLQRSAYLELLDCPNPSLWA   750
 751  VKKFVHLLNGTATIEEVQNQLESCQASLDSENMKKERLLKSIRQQLNING   800
 801  VLDKFGLLKDKDHELGISDSTIPKSKYQKYEKLFYMLQVDPSYWKLLYLK   850
 851  EPEFVAKNVYMTFGTVNQRMNDRERSYFTRFVCEMLQNAINEAPSIESFL   900
 901  DNRSQFWQTILQDFLRRESPEFFSIIVPVLDYLSDPVVDFESDPYKIYQE   950
 951  IHGFSSPQHCSPVDDASTKNKFIDNLRCLWHAIEMVAEIYTRKVHTIPVE  1000
1001  IRYLCTKIFCYAADKNIEEIDSLRAISSILVNVFVSEYLVNREYYGYKDS  1050
1051  NVQKNNQKIDILMKSLATVFEIKNFDGFLDPLNQYANEIKPHIKDVLYNV  1100
1101  LVDPEYEQEGDRLIYLDMVSPSPKLELLTEKVLEISGKFEEYLNEFPEAD  1150
1151  ILHDILEKNLDNSSFPRSGRVTLELDASAYRFLVSDDKMRKIYDQVKRAF  1200
1201  VYMMQIEDVDTNLYDLSISTILPQDEPNFANFLEQNPKIRDDPMIQKLKP  1250
1251  LKYFTLKNVTLKKIHELESTGTFCSSDNKLQNFLNDIANTIKNPNYAIDY  1300
1301  VTQEIYITKETLTKISEMNHSLDIELSRLKKHVDHTIKDFQKAKDFSPVH  1350
1351  KSKFGNFKNAVKKVQGRERSELQGMKFKWNTKQLYERGVLKTIRGEKLAE  1400
1401  LTVKVFGSSGPKFPDIIFKISTSDGSRFGIQMIDKRKGPDKRYSDDVDSF  1450
1451  SFKDLIKTQVEPKIETWKLFHSNVVVNNSQLLHLIVSFFYKRNAL       1495

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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