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

NucPred

Fetching Q64449 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MVPIRPALAPWPRHLLRCVLLLGGLRLGHPADSAAALLEPDVFLIFSQGM    50
  51  QGCLEAQGVQVRVTPVCNASLPAQRWKWVSRNRLFNLGATQCLGTGWPVT   100
 101  NTTVSLGMYECDREALSLRWQCRTLGDQLSLLLGARASNASKPGTLERGD   150
 151  QTRSGHWNIYGSEEDLCARPYYEVYTIQGNSHGKPCTIPFKYDNQWFHGC   200
 201  TSTGREDGHLWCATTQDYGKDERWGFCPIKSNDCETFWDKDQLTDSCYQF   250
 251  NFQSTLSWREAWASCEQQGADLLSITEIHEQTYINGLLTGYSSTLWIGLN   300
 301  DLDTSGGWQWSDNSPLKYLNWESDQPDNPGEENCGVIRTESSGGWQNHDC   350
 351  SIALPYVCKKKPNATVEPIQPDRWTNVKVECDPSWQPFQGHCYRLQAEKR   400
 401  SWQESKRACLRGGGDLLSIHSMAELEFITKQIKQEVEELWIGLNDLKLQM   450
 451  NFEWSDGSLVSFTHWHPFEPNNFRDSLEDCVTIWGPEGRWNDSPCNQSLP   500
 501  SICKKAGRLSQGAAEEDHGCRKGWTWHSPSCYWLGEDQVIYSDARRLCTD   550
 551  HGSQLVTITNRFEQAFVSSLIYNWEGEYFWTALQDLNSTGSFRWLSGDEV   600
 601  IYTHWNRDQPGYRRGGCVALATGSAMGLWEVKNCTSFRARYICRQSLGTP   650
 651  VTPELPGPDPTPSLTGSCPQGWVSDPKLRHCYKVFSSERLQEKKSWIQAL   700
 701  GVCRELGAQLLSLASYEEEHFVAHMLNKIFGESEPESHEQHWFWIGLNRR   750
 751  DPREGHSWRWSDGLGFSYHNFARSRHDDDDIRGCAVLDLASLQWVPMQCQ   800
 801  TQLDWICKIPRGVDVREPDIGRQGRLEWVRFQEAEYKFFEHHSSWAQAQR   850
 851  ICTWFQADLTSVHSQAELDFLGQNLQKLSSDQEQHWWIGLHTLESDGRFR   900
 901  WTDGSIINFISWAPGKPRPIGKDKKCVYMTARQEDWGDQRCHTALPYICK   950
 951  RSNSSGETQPQDLPPSALGGCPSGWNQFLNKCFRIQGQDPQDRVKWSEAQ  1000
1001  FSCEQQEAQLVTIANPLEQAFITASLPNVTFDLWIGLHASQRDFQWIEQE  1050
1051  PLLYTNWAPGEPSGPSPAPSGTKPTSCAVILHSPSAHFTGRWDDRSCTEE  1100
1101  THGFICQKGTDPSLSPSPAATPPAPGAELSYLNHTFRLLQKPLRWKDALL  1150
1151  LCESRNASLAHVPDPYTQAFLTQAARGLQTPLWIGLASEEGSRRYSWLSE  1200
1201  EPLNYVSWQDEEPQHSGGCAYVDVDGTWRTTSCDTKLQGAVCGVSRGPPP  1250
1251  RRINYRGSCPQGLADSSWIPFREHCYSFHMEVLLGHKEALQRCQKAGGTV  1300
1301  LSILDEMENVFVWEHLQTAEAQSRGAWLGMNFNPKGGTLVWQDNTAVNYS  1350
1351  NWGPPGLGPSMLSHNSCYWIQSSSGLWRPGACTNITMGVVCKLPRVEENS  1400
1401  FLPSAALPESPVALVVVLTAVLLLLALMTAALILYRRRQSAERGSFEGAR  1450
1451  YSRSSHSGPAEATEKNILVSDMEMNEQQE                       1479

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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