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

NucPred

Fetching Q02294 from www.uniprot.org...

The NucPred score for your sequence is 0.65 (see score help below)

   1  MVRFGDELGGRYGGTGGGERARGGGAGGAGGPGQGGLPPGQRVLYKQSIA    50
  51  QRARTMALYNPIPVKQNCFTVNRSLFVFSEDNVVRKYAKRITEWPPFEYM   100
 101  ILATIIANCIVLALEQHLPDGDKTPMSERLDDTEPYFIGIFCFEAGIKII   150
 151  ALGFVFHKGSYLRNGWNVMDFVVVLTEILATAGTDFDLRTLRAVRVLRPL   200
 201  KLVSGIPSLQVVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYMGKFH   250
 251  KACFPNSTDAEPVGDFPCGKEAPARLCDSDTECREYWPGPNFGITNFDNI   300
 301  LFAILTVFQCITMEGWTDILYNTNDAAGNTWNWLYFIPLIIIGSFFMLNL   350
 351  VLGVLSGEFAKERERVENRRAFLKLRRQQQIERELNGYLEWIFKAEEVML   400
 401  AEEDKNAEEKSPLDAVLKRAATKKSRNDLIHAEEGEDRFVDLCAAGSPFA   450
 451  RASLKSGKTESSSYFRRKEKMFRFLIRRMVKAQSFYWVVLCVVALNTLCV   500
 501  AMVHYNQPQRLTTALYFAEFVFLGLFLTEMSLKMYGLGPRSYFRSSFNCF   550
 551  DFGVIVGSIFEVVWAAIKPGTSFGISVLRALRLLRIFKVTKYWNSLRNLV   600
 601  VSLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFQDETPTTNFDTF   650
 651  PAAILTVFQILTGEDWNAVMYHGIESQGGVSKGMFSSFYFIVLTLFGNYT   700
 701  LLNVFLAIAVDNLANAQELTKDEEEMEEAANQKLALQKAKEVAEVSPMSA   750
 751  ANISIAARQQNSAKARSVWEQRASQLRLQNLRASCEALYSEMDPEERLRY   800
 801  ASTRHVRPDMKTHMDRPLVVEPGRDGLRGPAGNKSKPEGTEATEGADPPR   850
 851  RHHRHRDRDKTSASTPAGGEQDRTDCPKAESTETGAREERARPRRSHSKE   900
 901  APGADTQVRCERSRRHHRRGSPEEATEREPRRHRAHRHAQDSSKEGKEGT   950
 951  APVLVPKGERRARHRGPRTGPRETENSEEPTRRHRAKHKVPPTLEPPERE  1000
1001  VAEKESNVVEGDKETRNHQPKEPRCDLEAIAVTGVGSLHMLPSTCLQKVD  1050
1051  EQPEDADNQRNVTRMGSQPSDPSTTVHVPVTLTGPPGEATVVPSANTDLE  1100
1101  GQAEGKKEAEADDVLRRGPRPIVPYSSMFCLSPTNLLRRFCHYIVTMRYF  1150
1151  EMVILVVIALSSIALAAEDPVRTDSFRNNALKYMDYIFTGVFTFEMVIKM  1200
1201  IDLGLLLHPGAYFRDLWNILDFIVVSGALVAFAFSSFMGGSKGKDINTIK  1250
1251  SLRVLRVLRPLKTIKRLPKLKAVFDCVVNSLKNVLNILIVYMLFMFIFAV  1300
1301  IAVQLFKGKFFYCTDESKELERDCRGQYLDYEKEEVEAQPRQWKKYDFHY  1350
1351  DNVLWALLTLFTVSTGEGWPMVLKHSVDATYEEQGPSPGFRMELSIFYVV  1400
1401  YFVVFPFFFVNIFVALIIITFQEQGDKVMSECSLEKNERACIDFAISAKP  1450
1451  LTRYMPQNKQSFQYKTWTFVVSPPFEYFIMAMIALNTVVLMMKFYDAPYE  1500
1501  YELMLKCLNIVFTSMFSLECILKIIAFGVLNYFRDAWNVFDFVTVLGSIT  1550
1551  DILVTEIANNFINLSFLRLFRAARLIKLCRQGYTIRILLWTFVQSFKALP  1600
1601  YVCLLIAMLFFIYAIIGMQVFGNIALDDGTSINRHNNFRTFLQALMLLFR  1650
1651  SATGEAWHEIMLSCLGNRACDPHANASECGSDFAYFYFVSFIFLCSFLML  1700
1701  NLFVAVIMDNFEYLTRDSSILGPHHLDEFIRVWAEYDPAACGRISYNDMF  1750
1751  EMLKHMSPPLGLGKKCPARVAYKRLVRMNMPISNEDMTVHFTSTLMALIR  1800
1801  TALEIKLAPAGTKQHQCDAELRKEISSVWANLPQKTLDLLVPPHKPDEMT  1850
1851  VGKVYAALMIFDFYKQNKTTRDQTHQAPGGLSQMGPVSLFHPLKATLEQT  1900
1901  QPAVLRGARVFLRQKSATSLSNGGAIQTQESGIKESLSWGTQRTQDVLYE  1950
1951  ARAPLERGHSAEIPVGQPGALAVDVQMQNMTLRGPDGEPQPGLESQGRAA  2000
2001  SMPRLAAETQPAPNASPMKRSISTLAPRPHGTQLCNTVLDRPPPSQVSHH  2050
2051  HHHRCHRRRDKKQRSLEKGPSLSVDTEGAPSTAAGSGLPHGEGSTGCRRE  2100
2101  RKQERGRSQERRQPSSSSSEKQRFYSCDRFGSREPPQPKPSLSSHPISPT  2150
2151  AALEPGPHPQGSGSVNGSPLMSTSGASTPGRGGRRQLPQTPLTPRPSITY  2200
2201  KTANSSPVHFAEGQSGLPAFSPGRLSRGLSEHNALLQKEPLSQPLASGSR  2250
2251  IGSDPYLGQRLDSEASAHNLPEDTLTFEEAVATNSGRSSRTSYVSSLTSQ  2300
2301  SHPLRRVPNGYHCTLGLSTGVRARHSYHHPDQDHWC                2336

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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