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

NucPred

Fetching Q64535 from www.uniprot.org...

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

   1  MPEQERKVTAKEASRKILSKLALPTRPWGQSMKQSFAFDNVGYEGGLDST    50
  51  CFILQLTTGVVSILGMTCHSCVKSIEDRISSLKGIVSIKVSLEQGSATVK   100
 101  YVPSVLNLQQICLQIEDMGFEASAAEGKAASWPSRSSPAQEAVVKLRVEG   150
 151  MTCQSCVSSIEGKIRKLQGVVRVKVSLSNQEAVITYQPYLIQPEDLRDHI   200
 201  CDMGFEAAIKNRTAPLRLGPIDINKLESTNLKRAAVPPIQNSNHLETPGH   250
 251  QQNHLATLPLRIDGMHCKSCVLNIEGNIGQLPGVQNIHVSLENKTAQVQY   300
 301  DSSCITPLFLQTAIEALPPGYFKVSLPDGLEKESGSSSVPSLGSSQRQQE   350
 351  PGPCRTAVLTITGIPRDSSVQPMEDMLSQMKGVQQIDISLAEGTGAVLYD   400
 401  PSVVSSDELRTAVEDMGFEVSVNPENITTNRVSSGNSVPQAVGDSPGSVQ   450
 451  NMASDTRGLLTHQGPGYLSDSPPSPGGTASQKCFVQIKGMTCASCVSNIE   500
 501  RSLQRHAGILSVLVALMSGKAEVKYDPEVIQSPRIAQLIEDLGFEAAIME   550
 551  DNTVSEGDIELIITGMTCASCVHNIESKLTRTNGITYASVALATSKAHVK   600
 601  FDPEIIGPRDIIKVIEEIGFHASLAHRNPNAHHLDHKTEIKQWKKSFLCS   650
 651  LVFGIPVMGLMIYMLIPSSKPHETMVLDHNIIPGLSVLNLIFFILCTFVQ   700
 701  FLGGWYFYVQAYKSLRHKSANMDVLIVLATTIAYAYSLVILVVAIAEKAE   750
 751  KSPVTFFDTPPMLFVFIALGRWLEHVAKSKTSEALAKLMSLQATEATVVT   800
 801  LGEDNLILREEQVPMELVQRGDIIKVVPGGKFPVDGKVLEGNTMADESLI   850
 851  TGEAMPVTKKPGSIVIAGSINAHGSVLIKATHVGNDTTLAQIVKLVEEAQ   900
 901  MSKAPIQQLADRFSGYFVPFIIIISTLTLVVWIIIGFVDFGIVQKYFPSP   950
 951  SKHISQTEVIIRFAFQTSITVLCIACPCSLGLATPTAVMVGTGVAAQNGV  1000
1001  LIKGGKPLEMAHKIKTVMFDKTGTITHGVPRVMRFLLLVDVATLSLRKVL  1050
1051  AVVGTAEASSEHPLGVAVTKYCKEELGTETLGYSTDFQAVPGCGISCKVS  1100
1101  NVESILAHRGPTAHPIGVGNPPIGEGTGPQTFSVLIGNREWMRRNGLTIS  1150
1151  SDISDAMTDHEMKGQTAILVAIDGVLCGMIAIADAVKPEAALASITLKSM  1200
1201  GVDVALITGDNRKTARAIATQVGINKVFAEVLPSHKVAKVQELQNKGKKV  1250
1251  AMVGDGVNDSPALAQADVGIAIGTGTDVAIDAADVVLIRNDLLDVVASIH  1300
1301  LSKRTVRRIRVNLVLALIYNMVGIPIAAGVFMPIGIVLQPWMGSAAASSV  1350
1351  SVVLSSLQLKCYRKPDLERYEAQAHGRMKPLSASQVSVHVGMDDRRRDSP  1400
1401  RATPWDQVSYVSQVSLSSLTSDRLSRHGGMAEDGGDKWSLLLSDRDEEQC  1450
1451  I                                                   1451

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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