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

NucPred

Fetching O02811 from www.uniprot.org...

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

   1  MAAAAARGGGGGGGGGSFGSGAGGGASRGFYFNTVLSLARSLAVQRPASL    50
  51  EKVQKLLCMCPVDFHGIFQLDERRRDAVIALGIFLIESDLQHKDSVVPYL   100
 101  LRLLKGLPKVYWVEESTARKGRGTLPVAESFSFCLVTLLSDVAYRDPSLR   150
 151  GEILEALLQVLHVLLGMCQALEIQEKEYLCKHAVPCLLGIVRAFGRHSSS   200
 201  EDSILSRLFPRAPAHSPRVPEELEGVRRRSFNDFRSILPSSLLTVCQEGS   250
 251  LKRKASSASSVAQVSPERGAPPPSPPGGSAFHCLEASYSPNGSTSESDYY   300
 301  FSAVSSSFSVSPLFNGVTYKEFSIPLEMLRELLNLVKKIVEEPVLKSLDA   350
 351  VVTGVIEASPSADLCYGAFSDPLYVAVLRMLRDTLYYMRDLPTSFVKEVH   400
 401  DFVLEQFNSSQGELQKILHDADRAHSELSPLKLRCQASAACVDLMVWAVK   450
 451  DEQGAENLCVKLSEKLQSKTSSKVIIAHLPLLICCLQGLGRLCERFPVVV   500
 501  HSVTPSLRDFLVVPSPVLVKLYKCHSQYHTVAGNDIKISVTNEHAESTLN   550
 551  VASGKKSQPSMYEQLRDIAIDNVCRCLKAGLTVDPVIVEAFLASLSNRLY   600
 601  ISQESDKDAHLIPDHTIRALGHIAVALRDTPKVMEPILQILQQKFCQPPS   650
 651  PLDVLIIDQLGCLVITGNQYIYQEVWNLFQQISVKASSVVYSATKDYKDH   700
 701  GYRHCSLAVINALANIAANIQDEHLVDELLMNLLELFVQLGLEGKRASER   750
 751  ASEKGPALKASSSAGNLGVLIPVIAVLTRRLPPIKEPKPRLQKLFRDFWL   800
 801  YSVLMGFAVEGSGLWPEEWYEGVCEIATKSPLLTFPSKEPLRSVLQYNSA   850
 851  MKNDTVTPAELSELRSTIVNLLDPAPEVSALIGKLDFAMSTYLLSVYRLE   900
 901  YMRVLRSSDPARFQVMFCYFEDKAIQKDKSGMMQCVIAVADKVFDAFLNM   950
 951  MAEKAKTKENEEELERHAQFLLVSFNHVHKRIRRVADKYLSGLVDKFPHL  1000
1001  LWSGTVLKTMLDILQTLSLSLSADIHKDQPYYDIPDVPYRITVPDTYEAR  1050
1051  ESIVKDFAARCGMILQEAMKWAPTVTKSHLQEYLSKHQNWVSGLSQHTGL  1100
1101  AMATESVLHYAGYNKQSTSLGATQLTERPACVKKDYSNFMASLNLRNRYA  1150
1151  GEVYGMIRFSDATGHTSDLNKMMVQELKAALGAGDAQQYTQAMFKLTAML  1200
1201  ISSRDCDPQLLHHLCWGPLQMFNEHGMETALACWEWLLAGKNGVEVPFMR  1250
1251  EMAGAWQMTVEQKFGLFSAEMKEADPLAASEASQPKPCAPEVTPHYIWID  1300
1301  FLVQRFEIAKYCSSDQVEIFCSLLQRSLSLSIGGTAGSMNRHVAAIGPRF  1350
1351  KLLTLGLSLLHADVLPNATIRNVLREKIYSTAFDYFSCPPRFPTQGEKRL  1400
1401  REDISVMIKFWTAMFSDKKYLTASQLVPPDNQDTRSNLDIAVGSRQQATQ  1450
1451  GWINTYPLSSGMSTISKKSGMSKKTNRGSQLHKYYMKRRTLLLSLLATEI  1500
1501  ERLITWYNPLSAPELELDQAGESSVANWRSKYISLSEKQWKDNVNLAWSI  1550
1551  SPHLAVQLPARFKNTEAIGNEVTRLVRLDPGAVSDVPEAIKFLVTWHTID  1600
1601  ADAPELSHVLCWAPADPPTGLSYFSSMYPPHPLTAQYGVKVLRSFPPDAI  1650
1651  LFYIPQIVQALRYDKMGYVREYILWAASQSQLLAHQFIWNMKTNIYVDEE  1700
1701  GHQKDPDIGDLLEQLVEEITGSLSGPAKDFYQREFDFFNKITNVSAIIKP  1750
1751  YPKGDERKKACLSALSEVKVQPGCYLPSNPEAIVLDIDYKSGTPMQSAAK  1800
1801  APYLAKFKVKRCGVSELEKEGLRCRSDPEEEGSMQEADGQKISWQAAIFK  1850
1851  VGDDCRQDMLALQIIDLFKNIFQLVGLDLFVFPYRVVATAPGCGVIECIP  1900
1901  DCTSRDQLGRQTDFGMYDYFTRQYGDESTLAFQQARYNFIRSMAAYSLLL  1950
1951  FLLQIKDRHNGNIMLDKKGHLIHIDFGFMFESSPGGNLGWEPDIKLTDEM  2000
2001  VMIMGGKMEATPFKWFMEMCVRGYLAVRPYMDAVVSLVTLMLDTGLPCFR  2050
2051  GQTIKLLKHRFSPNMTEREAANFILKVIQNCFLSNRSRTYDMIQYYQNDI  2100
2101  PY                                                  2102

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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