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

NucPred

Fetching Q9HF61 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MLTAKQDEVGRELRVATGTSLIEYPVKDWLLRRQPTEWEALLGEAAIFSG    50
  51  QDELLWGPFVACVYREPRTTRLNCLFMDRIGVMHLHSVDVSDTSRFYPAV   100
 101  ENLRPEYRTQVVRRCLAVGLLKKYVLLDPSAVRLIRAELPYDYDQTTAGD   150
 151  LANTCELVEGQAARDVGQLLVRLGLVQPRHVRSLMLDVVYENHADVVDAN   200
 201  NKLVYYLGEQLEQLFDPLTEYSPEPTELSYRVPDQVRTSLSDEMPLMVSI   250
 251  CEELLQLQTNFTLSLVGFLQKFLIPLRIKALNEQVPGLSTVKLNNIFPPT   300
 301  IDEVTRINCIFLDALKAALPYGSLEVLKACSITAPYFYKAYTRHEAATKF   350
 351  FSRDIKSFLSTFGKSLSDLNFYSEIKLDTLIHGPQEKLTKLKLIIDRLFD   400
 401  SKDWETNEEQKEADRCYRSICDVIDSFGKDEPPNTYDTRVFTPSGKILTE   450
 451  LAKGWPAELQYKWLKRRVVGVFDVISVTDPESRDIVVIFSDYIVFLHVIN   500
 501  GNLYYSGDSKKPLISDVLMNSLINEVPLPPKIPKLEVLSHSYIDDVVVST   550
 551  YGKNSLRFDTLNAERPSSVAYTLASSSVEASYVADLCTKARILEKDTAFH   600
 601  LFKTAIDSFHVYSTAHESEAYKTERIKSPFVLFLNIPDSIGALQDHNATV   650
 651  GLFASLNKNDKVTLVRLGLDGSREESFASLDNFLSLIIEELLIFYPSYLS   700
 701  SATSPLFQQLMQINEQLVQTLLDPKGVHSASKSKCALRTSKKKKMPANLV   750
 751  STNDNSRTLSPGTIISRTPRTISTITPKQEKRKSVGQASNSPARGSISTT   800
 801  PRKHKRESILGKISGLFHKKDKKENKRNSVGSDTRNRHDNGSVHILRNSS   850
 851  SSFRELESPRQMKRFSSVVHTAVPSSSKRRTSGISPSKGTVNLRALQDAE   900
 901  NDDNADISKIPIPEGESLFDDTIRVDGVDADFYAQKDRLSKIYNHDLYGE   950
 951  VVPSAPGSKNVNVVSGATREQEKQQNTQKAIARELLASVDQQKRQPTHSA  1000
1001  PAESQIVIPGLPQSNVPQINFGRSPSFIELFGGMRLVLDENDESVNWRRL  1050
1051  CSERSLNEKYQIRPATYAGCISGELAPPVGIISDQRDSNLSGDNDADTPL  1100
1101  PMHSSNKSILSDETLEKGEFERDFAISTPKSQTVSDVNARRETWGYSHSH  1150
1151  DEEIDSEKRANTKPVSAPAPNVIPGLIITANSPTKPWHKENTRIKVSDVR  1200
1201  SEGTDVSYISSLKKSSNRLVELSVNSQEDFEDERHTPVIEPIQNPEAPSL  1250
1251  IENTETAPVASNSSNEETLSKLLGSQGVIDLTEETIDYSSINRKHASIQT  1300
1301  AYPVLDDVEFSTFHMSFGDMKAEDSHLANQRESYLFSNSTIAGKKDESHG  1350
1351  PVFYKLPDFVADDSYLGYSAVDQHAKHERNTEIGEEDEAMWVSPSKLDIF  1400
1401  DLSKQPESVYKRTSIPAKHAELLSKMRKDGSVKFEESMFIRDNSYVYLGQ  1450
1451  FLSADEVIEQQDKKLAANTDEMDSARRL                        1478

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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