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

NucPred

Fetching Q8N3C0 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MALPRLTGALRSFSNVTKQDNYNEEVADLKIKRSKLHEQVLDLGLTWKKI    50
  51  IKFLNEKLEKSKMQSINEDLKDILHAAKQIVGTDNGREAIESGAAFLFMT   100
 101  FHLKDSVGHKETKAIKQMFGPFPSSSATAACNATNRIISHFSQDDLTALV   150
 151  QMTEKEHGDRVFFGKNLAFSFDMHDLDHFDELPINGETQKTISLDYKKFL   200
 201  NEHLQEACTPELKPVEKTNGSFLWCEVEKYLNSTLKEMTEVPRVEDLCCT   250
 251  LYDMLASIKSGDELQDELFELLGPEGLELIEKLLQNRITIVDRFLNSSND   300
 301  HRFQALQDNCKKILGENAKPNYGCQVTIQSEQEKQLMKQYRREEKRIARR   350
 351  EKKAGEDLEVSEGLMCFDPKELRIQREQALLNARSVPILSRQRDADVEKI   400
 401  HYPHVYDSQAEAMKTSAFIAGAKMILPEGIQRENNKLYEEVRIPYSEPMP   450
 451  LSFEEKPVYIQDLDEIGQLAFKGMKRLNRIQSIVFETAYNTNENMLICAP   500
 501  TGAGKTNIAMLTVLHEIRQHFQQGVIKKNEFKIVYVAPMKALAAEMTDYF   550
 551  SRRLEPLGIIVKELTGDMQLSKSEILRTQMLVTTPEKWDVVTRKSVGDVA   600
 601  LSQIVRLLILDEVHLLHEDRGPVLESIVARTLRQVESTQSMIRILGLSAT   650
 651  LPNYLDVATFLHVNPYIGLFFFDGRFRPVPLGQTFLGIKCANKMQQLNNM   700
 701  DEVCYENVLKQVKAGHQVMVFVHARNATVRTAMSLIERAKNCGHIPFFFP   750
 751  TQGHDYVLAEKQVQRSRNKQVRELFPDGFSIHHAGMLRQDRNLVENLFSN   800
 801  GHIKVLVCTATLAWGVNLPAHAVIIKGTQIYAAKRGSFVDLGILDVMQIF   850
 851  GRAGRPQFDKFGEGIIITTHDKLSHYLTLLTQRNPIESQFLESLADNLNA   900
 901  EIALGTVTNVEEAVKWISYTYLYVRMRANPLAYGISHKAYQIDPTLRKHR   950
 951  EQLVIEVGRKLDKAQMIRFEERTGYFSSTDLGRTASHYYIKYNTIETFNE  1000
1001  LFDAHKTEGDIFAIVSKAEEFDQIKVREEEIEELDTLLSNFCELSTPGGV  1050
1051  ENSYGKINILLQTYISRGEMDSFSLISDSAYVAQNAARIVRALFEIALRK  1100
1101  RWPTMTYRLLNLSKVIDKRLWGWASPLRQFSILPPHILTRLEEKKLTVDK  1150
1151  LKDMRKDEIGHILHHVNIGLKVKQCVHQIPSVMMEASIQPITRTVLRVTL  1200
1201  SIYADFTWNDQVHGTVGEPWWIWVEDPTNDHIYHSEYFLALKKQVISKEA  1250
1251  QLLVFTIPIFEPLPSQYYIRAVSDRWLGAEAVCIINFQHLILPERHPPHT  1300
1301  ELLDLQPLPITALGCKAYEALYNFSHFNPVQTQIFHTLYHTDCNVLLGAP  1350
1351  TGSGKTVAAELAIFRVFNKYPTSKAVYIAPLKALVRERMDDWKVRIEEKL  1400
1401  GKKVIELTGDVTPDMKSIAKADLIVTTPEKWDGVSRSWQNRNYVQQVTIL  1450
1451  IIDEIHLLGEERGPVLEVIVSRTNFISSHTEKPVRIVGLSTALANARDLA  1500
1501  DWLNIKQMGLFNFRPSVRPVPLEVHIQGFPGQHYCPRMASMNKPAFQAIR  1550
1551  SHSPAKPVLIFVSSRRQTRLTALELIAFLATEEDPKQWLNMDEREMENII  1600
1601  ATVRDSNLKLTLAFGIGMHHAGLHERDRKTVEELFVNCKVQVLIATSTLA  1650
1651  WGVNFPAHLVIIKGTEYYDGKTRRYVDFPITDVLQMMGRAGRPQFDDQGK  1700
1701  AVILVHDIKKDFYKKFLYEPFPVESSLLGVLSDHLNAEIAGGTITSKQDA  1750
1751  LDYITWTYFFRRLIMNPSYYNLGDVSHDSVNKFLSHLIEKSLIELELSYC  1800
1801  IEIGEDNRSIEPLTYGRIASYYYLKHQTVKMFKDRLKPECSTEELLSILS  1850
1851  DAEEYTDLPVRHNEDHMNSELAKCLPIESNPHSFDSPHTKAHLLLQAHLS  1900
1901  RAMLPCPDYDTDTKTVLDQALRVCQAMLDVAANQGWLVTVLNITNLIQMV  1950
1951  IQGRWLKDSSLLTLPNIENHHLHLFKKWKPIMKGPHARGRTSIESLPELI  2000
2001  HACGGKDHVFSSMVESELHAAKTKQAWNFLSHLPVINVGISVKGSWDDLV  2050
2051  EGHNELSVSTLTADKRDDNKWIKLHADQEYVLQVSLQRVHFGFHKGKPES  2100
2101  CAVTPRFPKSKDEGWFLILGEVDKRELIALKRVGYIRNHHVASLSFYTPE  2150
2151  IPGRYIYTLYFMSDCYLGLDQQYDIYLNVTQASLSAQVNTKVSDSLTDLA  2200
2201  LK                                                  2202

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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