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

NucPred

Fetching Q86VI3 from www.uniprot.org...

The NucPred score for your sequence is 0.60 (see score help below)

   1  MERRAAGPGWAAYERLTAEEMDEQRRQNVAYQYLCRLEEAKRWMEACLKE    50
  51  ELPSPVELEESLRNGVLLAKLGHCFAPSVVPLKKIYDVEQLRYQATGLHF   100
 101  RHTDNINFWLSAIAHIGLPSTFFPETTDIYDKKNMPRVVYCIHALSLFLF   150
 151  RLGLAPQIHDLYGKVKFTAEELSNMASELAKYGLQLPAFSKIGGILANEL   200
 201  SVDEAAVHAAVLAINEAVERGVVEDTLAALQNPSALLENLREPLAAVYQE   250
 251  MLAQAKMEKAANARNHDDRESQDIYDHYLTQAEIQGNINHVNVHGALEVV   300
 301  DDALERQSPEALLKALQDPALALRGVRRDFADWYLEQLNSDREQKAQELG   350
 351  LVELLEKEEVQAGVAAANTKGDQEQAMLHAVQRINKAIRRRVAADTVKEL   400
 401  MCPEAQLPPVYPVASSMYQLELAVLQQQQGELGQEELFVAVEMLSAVVLI   450
 451  NRALEARDASGFWSSLVNPATGLAEVEGENAQRYFDALLKLRQERGMGED   500
 501  FLSWNDLQATVSQVNAQTQEETDRVLAVSLINEALDKGSPEKTLSALLLP   550
 551  AAGLDDVSLPVAPRYHLLLVAAKRQKAQVTGDPGAVLWLEEIRQGVVRAN   600
 601  QDTNTAQRMALGVAAINQAIKEGKAAQTERVLRNPAVALRGVVPDCANGY   650
 651  QRALESAMAKKQRPADTAFWVQHDMKDGTAYYFHLQTFQGIWEQPPGCPL   700
 701  NTSHLTREEIQSAVTKVTAAYDRQQLWKANVGFVIQLQARLRGFLVRQKF   750
 751  AEHSHFLRTWLPAVIKIQAHWRGYRQRKIYLEWLQYFKANLDAIIKIQAW   800
 801  ARMWAARRQYLRRLHYFQKNVNSIVKIQAFFRARKAQDDYRILVHAPHPP   850
 851  LSVVRRFAHLLNQSQQDFLAEAELLKLQEEVVRKIRSNQQLEQDLNIMDI   900
 901  KIGLLVKNRITLQEVVSHCKKLTKRNKEQLSDMMVLDKQKGLKSLSKEKR   950
 951  QKLEAYQHLFYLLQTQPIYLAKLIFQMPQNKTTKFMEAVIFSLYNYASSR  1000
1001  REAYLLLQLFKTALQEEIKSKVEQPQDVVTGNPTVVRLVVRFYRNGRGQS  1050
1051  ALQEILGKVIQDVLEDKVLSVHTDPVHLYKNWINQTEAQTGQRSHLPYDV  1100
1101  TPEQALSHPEVQRRLDIALRNLLAMTDKFLLAITSSVDQIPYGMRYVAKV  1150
1151  LKATLAEKFPDATDSEVYKVVGNLLYYRFLNPAVVAPDAFDIVAMAAGGA  1200
1201  LAAPQRHALGAVAQLLQHAAAGKAFSGQSQHLRVLNDYLEETHLKFRKFI  1250
1251  HRACQVPEPEERFAVDEYSDMVAVAKPMVYITVGELVNTHRLLLEHQDCI  1300
1301  APDHQDPLHELLEDLGELPTIPDLIGESIAADGHTDLSKLEVSLTLTNKF  1350
1351  EGLEADADDSNTRSLLLSTKQLLADIIQFHPGDTLKEILSLSASREQEAA  1400
1401  HKQLMSRRQACTAQTPEPLRRHRSLTAHSLLPLAEKQRRVLRNLRRLEAL  1450
1451  GLVSARNGYQGLVDELAKDIRNQHRHRHRRKAELVKLQATLQGLSTKTTF  1500
1501  YEEQGDYYSQYIRACLDHLAPDSKSSGKGKKQPSLHYTAAQLLEKGVLVE  1550
1551  IEDLPASHFRNVIFDITPGDEAGKFEVNAKFLGVDMERFQLHYQDLLQLQ  1600
1601  YEGVAVMKLFNKAKVNVNLLIFLLNKKFLRK                     1631

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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