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

NucPred

Fetching P13055 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MEAVQAAAAATSSGGSSGSVPGSGSGSASKLIKTEPIDFEMLHLEENERQ    50
  51  QDIEREPSSSNSNSNSNSLTPQRYTHVQVQTVPPRQPTGLTTPGGTQKVI   100
 101  LTPRVEYVQQRATSSTGGGMKHVYSQQQGTAASRSAPPETTALLTTTSGT   150
 151  PQIIITRTLPSNQHLSRRHSASPSALHHYQQQQPQRQQSPPPLHHQQQQQ   200
 201  QQHVRVIRDGRLYDEATVVVAARRHSVSPPPLHHHSRSAPVSPVIARRGG   250
 251  AAAYMDQQYQQRQTPPLAPPPPPPPPPPPPPPPQQQQQQYISTGVPPPTA   300
 301  AARKFVVSTSTRHVNVIASNHFQQQQQQHQAQQHQQQHQQHQQHQQHVIA   350
 351  SVSSSSSSSAIGSGGSSSSHIFRTPVVSSSSSSNMHHQQQQQQQQSSLGN   400
 401  SVMRPPPPPPPPKVKHASSSSSGNSSSSNTNNSSSSSNGEEPSSSIPDLE   450
 451  FDGTTVLCRVCGDKASGFHYGVHSCEGCKGFFRRSIQQKIQYRPCTKNQQ   500
 501  CSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKREKARILAAMQQST   550
 551  QNRGQQRALATELDDQPRLLAAVLRAHLETCEFTKEKVSAMRQRARDCPS   600
 601  YSMPTLLACPLNPAPELQSEQEFSQRFAHVIRGVIDFAGMIPGFQLLTQD   650
 651  DKFTLLKAGLFDALFVRLICMFDSSINSIICLNGQVMRRDAIQNGANARF   700
 701  LVDSTFNFAERMNSMNLTDAEIGLFCAIVLITPDRPGLRNLELIEKMYSR   750
 751  LKGCLQYIVAQNRPDQPEFLAKLLETMPDLRTLSTLHTEKLVVFRTEHKE   800
 801  LLRQQMWSMEDGNNSDGQQNKSPSGSWADAMDVEAAKSPLGSVSSTESAD   850
 851  LDYGSPSSSQPQGVSLPSPPQQQPSALASSAPLLAATLSGGCPLRNRANS   900
 901  GSSGDSGAAEMDIVGSHAHLTQNGLTITPIVRHQQQQQQQQQIGILNNAH   950
 951  SRNLNGGHAMCQQQQQHPQLHHHLTAGAARYRKLDSPTDSGIESGNEKNE  1000
1001  CKAVSSGGSSSCSSPRSSVDDALDCSDAAANHNQVVQHPQLSVVSVSPVR  1050
1051  SPQPSTSSHLKRQIVEDMPVLKRVLQAPPLYDTNSLMDEAYKPHKKFRAL  1100
1101  RHREFETAEADASSSTSGSNSLSAGSPRQSPVPNSVATPPPSAASAAAGN  1150
1151  PAQSQLHMHLTRSSPKASMASSHSVLAKSLMAEPRMTPEQMKRSDIIQNY  1200
1201  LKRENSTAASSTTNGVGNRSPSSSSTPPPSAVQNQQRWGSSSVITTTCQQ  1250
1251  RQQSVSPHSNGSSSSSSSSSSSSSSSSSTSSNCSSSSASSCQYFQSPHST  1300
1301  SNGTSAPASSSSGSNSATPLLELQVDIADSAQPLNLSKKSPTPPPSKLHA  1350
1351  LVAAANAVQRYPTLSADVTVTASNGGPPSAAASPAPSSSPPASVGSPNPG  1400
1401  LSAAVHKVMLEA                                        1412

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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