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

NucPred

Fetching P41515 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MELSPLQPVNENMQMNKKKNEDAKKRLSIERIYQKKTQLEHILLRPDTYI    50
  51  GSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRDPK   100
 101  MSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNY   150
 151  DDDEKKVTGGRNGYGAKLCNIFSTRFTVETASKEYKKMFKQTWMDNMGRA   200
 201  GDMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTK   250
 251  DVKVFLNGNKLPVKGFRSYVDMYLKDKLDETGNALKVVHEQVNPRWEVCL   300
 301  TMSEKGFQQISFVNSIATSKGGRHVDYVADQIVSKLVDVVKKKNKGGVAV   350
 351  KAHQVKNHMWIFVNALIENPTFDSQTKENMTLQAKSFGSTCQLSEKFIKA   400
 401  AIGCGIVESILNWVKFKAQIQLNKKCSAVKHNRIKGIPKLDDANDAGSRN   450
 451  STECTLILTEGDSAKTLAVSGLGVVGRDKYGVFPLRGKILNVREASHKQI   500
 501  MENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGKIMIMTDQDQDGSHIKG   550
 551  LLINFIHHNWPSLLRHRFLEEFITPIVKVSKNKQELAFYSLPEFEEWKSS   600
 601  TPNHKKWKVKYYKGLGTSTSKEAKEYFADMKRHRIQFKYSGPEDDAAISL   650
 651  AFSKKQVDDRKEWLTHFMEDRRQRKLLGLPEDYLYGQTTTYLTYNDFINK   700
 701  ELILFSNSDNERSIPSMVDGLKPGQRKVLFTCFKRNDKREVKVAQLAGSV   750
 751  AEMSSYHHGEMSLMMTIINLAQNFVGSNNLNLLQPIGQFGTRLHGGKDSA   800
 801  SPRYIFTMLSPLTRLLFPPKDDHTLKFLYDDNQRVEPEWYIPIIPMVLIN   850
 851  GAEGIGTGWSCKIPNFDIREVVNNIRRLLDGEEPLPMLPSYKNFKGTIEE   900
 901  LASNQYVINGEVAILNSTTIEISELPIRTWTQTYKEQVLEPMLNGTEKTP   950
 951  PLITDYREYHTDTTVKFVIKMTEEKLAEAERVGLHKVFKLQTSLTCNSMV  1000
1001  LFDHVGCLKKYDTVLDILKDFFELRLKYYGLRKEWLLGMLGAESAKLNNQ  1050
1051  ARFILEKIDGKIIIENKPKKELIKVLIQRGYDSDPVKAWKEAQQKVPDEE  1100
1101  ENEESDNENSDSVAESGPTFNYLLDMPLWYLTKEKKDELCKQRNEKEQEL  1150
1151  NTLKNKSPSDLWKEDLAVFIEELEVVEAKEKQDEQVGLPGKGGKAKGKKA  1200
1201  QMSEVLPSPHGKRVIPQVTMEMKAEAEKKIRKKIKSENVEGTPTENGLEL  1250
1251  GSLKQRIEKKQKKEPGAMTKKQTTLAFKPIKKGKKRNPWSDSESDMSSNE  1300
1301  SNVDVPPREKDPRRAATKAKFTMDLDSDEDFSGSDGKDEDEDFFPLDTTP  1350
1351  PKTKIPQKNTKKALKPQKSAMSGDPESDEKDSVPASPGPPAADLPADTEQ  1400
1401  LKPSSKQTVAVKKTATKSQSSTSTAGTKKRAVPKGSKSDSALNAHGPEKP  1450
1451  VPAKAKNSRKRKQSSSDDSDSDFEKVVSKVAASKKSKGENQDFRVDLDET  1500
1501  MVPRAKSGRAKKPIKYLEESDDDDLF                          1526

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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