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

NucPred

Fetching P22276 from www.uniprot.org...

The NucPred score for your sequence is 0.63 (see score help below)

   1  MVAATKRRKTHIHKHVKDEAFDDLLKPVYKGKKLTDEINTAQDKWHLLPA    50
  51  FLKVKGLVKQHLDSFNYFVDTDLKKIIKANQLILSDVDPEFYLKYVDIRV   100
 101  GKKSSSSTKDYLTPPHECRLRDMTYSAPIYVDIEYTRGRNIIMHKDVEIG   150
 151  RMPIMLRSNKCILYDADESKMAKLNECPLDPGGYFIVNGTEKVILVQEQL   200
 201  SKNRIIVEADEKKGIVQASVTSSTHERKSKTYVITKNGKIYLKHNSIAEE   250
 251  IPIAIVLKACGILSDLEIMQLVCGNDSSYQDIFAVNLEESSKLDIYTQQQ   300
 301  ALEYIGAKVKTMRRQKLTILQEGIEAIATTVIAHLTVEALDFREKALYIA   350
 351  MMTRRVVMAMYNPKMIDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFK   400
 401  LSIDKVLKKPNRAMEYDALLSINVHSNNITSGLNRAISTGNWSLKRFKME   450
 451  RAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTA   500
 501  DTPEGEACGLVKNLALMTHITTDDEEEPIKKLCYVLGVEDITLIDSASLH   550
 551  LNYGVYLNGTLIGSIRFPTKFVTQFRHLRRTGKVSEFISIYSNSHQMAVH   600
 601  IATDGGRICRPLIIVSDGQSRVKDIHLRKLLDGELDFDDFLKLGLVEYLD   650
 651  VNEENDSYIALYEKDIVPSMTHLEIEPFTILGAVAGLIPYPHHNQSPRNT   700
 701  YQCAMGKQAIGAIAYNQFKRIDTLLYLMTYPQQPMVKTKTIELIDYDKLP   750
 751  AGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKRYAN   800
 801  HTQDIIGGMRVDENGDPIWQHQSLGPDGLGEVGMKVQSGQIYINKSVPTN   850
 851  SADAPNPNNVNVQTQYREAPVIYRGPEPSHIDQVMMSVSDNDQALIKVLL   900
 901  RQNRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGIVPDIIMNPHGFP   950
 951  SRMTVGKMIELISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDQGFNYSG  1000
1001  KDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQP  1050
1051  TEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCDKCGL  1100
1101  MGYSGWCTTCKSAENIIKMTIPYAAKLLFQELLSMNIAPRLRLEDIFQQ   1149

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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