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

NucPred

Fetching P41004 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSDKGIFRTSSTPSIVDVTPDRGERPRKLVRSVLESPSQKDVASIVKIEQ    50
  51  TPSRPFFNDFLKKRITDSLNERPNLLNKFMSAQDGTPSKSTGFNERSSQL   100
 101  VSEFTTTEDIENCEETTQVLPPRLVVYELRLTNFKSYAGTQIVGPFHPSF   150
 151  SSIVGPNGSGKSNVIDALLFVFGFRASKLRQSKASALIHKSATHPSLDSC   200
 201  DVEITFKEVNSDFTYVDGSELTVRRTAYKNNTSKYFVNGVESSFSAVSNL   250
 251  LKEKGIDLNHKRFLILQGEVESIAQMKPRAISEGDDGLLEYLEDIIGTSK   300
 301  YKPIIEENMQELSNSDDICAEKESRLKLVLSEKAKLEDSKNSVLSFLKDE   350
 351  NELFMKQNQLYRTILYETRNKKTLVQNLLNSLEGKLQAHLEKFEQTERDI   400
 401  SEKNEEVKSLREKAAKVKNDCTSEKKTRQSYEQQTVKIEEQLKFLLNKEK   450
 451  KLKKSIEALSFEKSEAENSLSSHDIDSQKLNSEIADLSLRLQQEELSLDD   500
 501  IRKSLQGKTEGISNAIEEKQKAMAPALEKINQLTSEKQILQVELDMLLNK   550
 551  ENDLINDVESSQSSLDKLRNDAEENRNILSSKLKVLSDLKGEKKDVSKNI   600
 601  ERKKETVHNTYRNLMSNRTKLEEMKASLSSSRSRGNVLESLQRLHESDNL   650
 651  NGFFGRLGDLATIDEAYDVAISTACPALNHIVVDNIETGQKCVAFLRSNN   700
 701  LGRASFIILKELAQKNLARIQTPENVPRLFDLLRFNDQKFAPAFYNVLQN   750
 751  TLVAKNLEQANRIAYGKTRWRVVTLSGQLIDKSGTMTGGGTRVKKGGMSS   800
 801  AITSDVSPASVETCDKQVQLEDTRYRQHLSELESLNQRFTEISERIPSAE   850
 851  LEISKLQLDVSACDRLVAGEERRILQLKSDLKSIRNNNERKRNLQNKISN   900
 901  MDKEVEAININNEGLVTEIKTLQDKIMEIGGIRYRIQKSKVDDLHEQLKF   950
 951  VKDKLNKMSFKKKKNEQRSQSFQVELSNLTSEYDTTTESIATLKTELQSL  1000
1001  NKYVDEHKSRLREFENALWDINSSIDELVKFIEFESKQMNSVKAERIELE  1050
1051  NQIQEQRTALSEVGNNENKYLKLMSNLKLHNLTEFCDQTTMDSTFPEYSE  1100
1101  DELSSVDKSELVSNISVLKKKTEDREVDINVLSEYRRCNKEAEKRDSDYQ  1150
1151  SELQKRTDLKKVVTDLQSQRLDEFMYGFGIISMKLKEMYQIITMGGNAEL  1200
1201  ELVDSLDPFSEGVLFSVMPPKKSWKNISNLSGGEKTLSSLALVFALHNYK  1250
1251  PTPLYVMDEIDAALDFKNVSIVANYIKERTKNAQFIVISLRSNMFELSSR  1300
1301  LVGIYKTANMTKSVTINNKEILTD                            1324

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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