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

NucPred

Fetching Q9Y3R5 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MDPEEQELLNDYRYRSYSSVIEKALRNFESSSEWADLISSLGKLNKALQS    50
  51  NLRYSLLPRRLLISKRLAQCLHPALPSGVHLKALETYEIIFKIVGTKWLA   100
 101  KDLFLYSCGLFPLLAHAAVSVRPVLLTLYEKYFLPLQKLLLPSLQAFIVG   150
 151  LLPGLEEGSEISDRTDALLLRLSLVVGKEVFYTALWGSVLASPSIRLPAS   200
 201  VFVVGHINRDAPGREQKYMLGTNHQLTVKSLRASLLDSNVLVQRNNLEIV   250
 251  LFFFPFYTCLDSNERAIPLLRSDIVRILSAATQTLLRRDMSLNRRLYAWL   300
 301  LGSDIKGNTVVPESEISNSYEDQSSYFFEKYSKDLLVEGLAEILHQKFID   350
 351  ADVEERHHAYLKPFRVLISLLDKPEIGPQVVGNLFLEVIRAFYSYCRDAL   400
 401  GSDLKLSYTQSGNSLISAIKENRNASEIVKTVNLLITSLSTDFLWDYMTR   450
 451  CFEECFRPVKQRYSVRNSVSPPPTVSELCALLVFLLDVIPLELYSEVQTQ   500
 501  YLPQVLGCLVQPLAEDMEALSLPELTHALKTCFKVLSKVQMPPSYLDTES   550
 551  TSGTSSPVKGENGKIILETKAVIPGDEDASFPPLKSEDSGIGLSASSPEL   600
 601  SEHLRVPRVSLERDDVWKKGGSMQRTFLCIQELIANFASKNIFGVQLTAS   650
 651  GEESKSEEPAGKRDRDGTQSLAANDSSRKNSWEPKPITVPQFKQMLSDLF   700
 701  TARGSPFKTKSSESPSSSPSSPARKNGGEWDVEKVVIDLGGSREERREAF   750
 751  AAACHLLLDCATFPVYLSEEETEQLCATLFQLPGAGDSSFPSWLKSLMTI   800
 801  CCCVTDCYLQNVAISTLLEVINHSQSLALVIEDKMKRYKSSGHNPFFGKL   850
 851  QMVTVPPIAPGILKVIAEKTDFYQRVARVLWNQLNKETREHHVTCVELFY   900
 901  RLHCLAPTANICEDIICHALLDPDKGTRLEALFRFSVIWHLTREIQGSRV   950
 951  TSHNRSFDRSLFVVLDSLACTDGAIGAAAQGWLVRALSLGDVARILEPVL  1000
1001  LLLLQPKTQRTSIHCLKQENSADDLHRWFNRKKTSFREACAVPEPQESGS  1050
1051  EEHLPLSQFTTVDREAIWAEVEKEPEKYPLRGELSEEELPYYVELPDRTA  1100
1101  HGAPDSSEHTESADTSSCHTDSENTSSFSSPSHDLQELSNEENCCAPIPM  1150
1151  GGRAYPKRSALLAAFQSESFKAGAKLSLVRVDSDKTQASESFSSDEEADL  1200
1201  ELQALTTSRLLKQQRERQEAVEALFKHILLYLQPYDSRRVLYAFSVLEAV  1250
1251  LKTNPKEFIEAVSRTSMDTSSTAHLNLISNLLARHQEALIGQSFYGKLQT  1300
1301  QVPNVCPHSLLLELLTYLCLSFLRSYYPCYLKVSHRDILGNRDVQVKSVE  1350
1351  VLIRIMMQLVSVAKSSEGKNVEFIHSLLQRCKVQEFVLLSLSASMYTSQK  1400
1401  RYGLATAHHGRALPEDSLFEESLINLGQDQIWSEHPLQIELLKLLQVLIV  1450
1451  LEHHLGRAHEEAENQPDLSREWQRALNFQQAISALQYVQPHPLTSQGLLV  1500
1501  SAVVRGLQPAYGYGMHPAWVSLVTHSLPYFGKSLGWTVTPFVVQICKNLD  1550
1551  DLVKQYESESVKLSVSTTSKRENISPDYPLTLLEGLTTISHFCLLEQANQ  1600
1601  NKKTMAAGDPANLRNARNAILEELPRTVNTMALLWNVLRKEETQKRPVDL  1650
1651  LGATKGSSSVYFKTTKTIRQKILDFLNPLTAHLGVQLTAAVAAVWSRKKA  1700
1701  QRHSKMKIIPTASASQLTLVDLVCALSTLQTDTLLHLVKEVVKRPPQVKG  1750
1751  GDEKSPLVDIPVLQFCYAFLQRLPVPALQENFSSLLGVLKESVQLNLAPP  1800
1801  GYFLLLSMLNDFVTRTPNLENKKDQKDLQEITQKILEAVGNIAGSSLEQT  1850
1851  SWLSRNLEVKAQPQASLEESDAEEDLYDAAAASAMVSSSAPSVYSVQALS  1900
1901  LLAEVLASLLDMVYRSDEKEKAVPLISRLLYYVFPYLRNHSAYNAPSFRA  1950
1951  GAQLLSSLSGYAYTKRAWRKEVLELFLDPAFFQMDTSCVHWKSIIDHLLT  2000
2001  HEKTMFKDLMNMQSSSLKLFSSFEQKAMLLKRQAFAVFSGELDQYHLYLP  2050
2051  LIQERLTDNLRVGQTSIVAAQMFLFFRVLLLRISPQHLTSLWPIMVSELI  2100
2101  QTFTQLEEDLKDEDESLRSTNKVNRTKVSVPDANGPSVGEIPQSELILYL  2150
2151  SACKFLDTALSFPPDKMPLFQIYRWAFIPEVDTEGPAFLSDVEENHQECK  2200
2201  PHTVRILELLKLKFGEISSSDEITMKSEFPLLRQHSVSSIRQLMPFFMTL  2250
2251  NGAFKTQRQLPADSPGTPFLDFPVTDSPRILKQLEECIEYDFLEHPEC    2298

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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