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

NucPred

Fetching Q05152 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MVRFGDELGGRYGGAGGAERARGGGAGGAGGPGPGGLPPGQRVLYKQSIA    50
  51  QRARTMALYNPIPVKQNCFTVNRSLFVFSEDNVVRKYAKRITEWPPFEYM   100
 101  ILATIIANCIVLALEQHLPDGDKTPMSERLDDTEPYFIGIFCFEAGIKIL   150
 151  ALGFVLHKGSYLRNGWNVMDFVVVLTGILATAGTDFDLRTLRAVRVLRPL   200
 201  KLVSGIPSLQVVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYMGKFH   250
 251  KACFPNSTDPDPVGDFPCGKEAPARLCEGDTECREYWAGPNFGITNFDNI   300
 301  LFAILTVFQCITMEGWTDILYNTNDAAGNTWNWLYFIPLIIIGSFFMLNL   350
 351  VLGVLSGEFAKERERVENRRAFLKLRRQQQIERELNGYLEWIFKAEEVML   400
 401  AEEDRNAEEKSPLDAVLKRAAAKKSRSDLIQAEEGEGRLTGLCAPGSPFA   450
 451  RASLKSGKTESSSYFRRKEKMFRFFIRRMVKAQSFYWTVLCVVALNTLCV   500
 501  AMVHYNQPQRLTTALYFAEFVFLGLFLTEMSLKMYGLGPRSYFRSSFNCF   550
 551  DFGVIVGSIFEVVWAAVKPGTSFGISVLRALRLLRIFKVTKYWNSLRNLV   600
 601  VSLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFKDETPTTNFDTF   650
 651  PAAILTVFQILTGEDWNAVMYHGIESQGGVSRGMFSSFYFIVLTLFGNYT   700
 701  LLNVFLAIAVDNLANAQELTKDEEEMEEAANQKLALQKAKEVAEVSPMSA   750
 751  ANISIAARQQNSAKARSVWEQRASQLRLQNLRASCEALYSEMDPEERLRY   800
 801  ATARHLRPDVKTHLDRPLVVEPGRDAPRGPPGGKSRPDGSEAPEGADPPR   850
 851  RHHRHRDKDKAPATVPSAGEQDRAEALRAEGGELGPREERGRPRRSRSKE   900
 901  APGAPEVRSDRGRGPCPEGGRRHHRRGSPEEAAEREPRRHRAHRHGPDPG   950
 951  KEGPASGTRGERRARHRTGPRACPREAESSEEPARRHRARHKAPPTQETA  1000
1001  EKDKEAAEKGGEATEAEKDKEARNHQPKELPCDLEAIGMLGVGAVHTLPS  1050
1051  TCLQKVEEQPEDADNQRNVTRMGSQPPDTSTTVHIPVTLTGPPGETTVVP  1100
1101  SGNVDLESQAEGKKEVETSDVMRSGPRPIVPYSSMFCLSPTNLLRRCCHY  1150
1151  IVTMRYFEMVILVVIALSSIALAAEDPVRTDSPRNNALKYMDYIFTGVFT  1200
1201  FEMVIKMIDLGLLLHPGAYFRDLWNILDFIVVSGALVAFAFSGSKGKDIS  1250
1251  TIKSLRVLRVLRPLKTIKRLPKLKAVFDCVVNSLKNVLNILIVYMLFMFI  1300
1301  FAVIAVQLFKGKFFYCTDESKELERDCRGQYLDYEKEEVEAQPRQWKKYD  1350
1351  FHYDNVLWALLTLFTVSTGEGWPMVLKHSVDATYEEQGPSPGYRMELSIF  1400
1401  YVVYFVVFPFFFVNIFVALIIITFQEQGDKVMSECSLEKNERACIDFAIS  1450
1451  ARPLTRYMPQNKQSFQYKTWTFVVSPPFEYFIMAMIALNTVVLMMKFYDA  1500
1501  PYEYELMLKCLNIVFTSMFSMECVLKIIAFGVLNYFRDAWNVFDFVTVLG  1550
1551  SITDILVTEIANNFINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFK  1600
1601  ALPYVCLLIAMLFFIYAIIGMQVFGNIALDDDTSINRHNNFRTFLQALML  1650
1651  LFRSATGEAWHEIMLSCLSSRACDEHSNASECGSDFAYFYFVSFIFLCSF  1700
1701  LMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFIRVWAEYDPAACGRISYS  1750
1751  DMFEMLKHMSPPLGLGKKCPARVAYKRLVRMNMPISSEDMTVHFTSTLMA  1800
1801  LIRTALDIKLAPAGTKQHQCDAELRKEISCVWANLPQKTLDLLVPPHKPD  1850
1851  EMTVGKVYAALMIFDFYKQNKTSRDQTQQAPGGLSQLGPVSLFHPLKATL  1900
1901  EQTQPALRGARAFLRQKSSASLSNGGAVQTQESGIKESVSWGTQRTQDVL  1950
1951  CEARAPLERGHSAEIPVGQPGTLAVDVQMQNMTLSGPDAEPQPGLESQGR  2000
2001  AASMPRLAAETQPAPDASPMKRSISTLAPRPHTARLGSTALDRPAPSQAP  2050
2051  HHHHHRCHRRRDRKQRSLEKGPSLSADTDGAPDSTVGPGLPTGEGPPGCR  2100
2101  RERERRQERGRSQERRQPSSSSSEKHRFYSCDRFGGREPPQPKPSLSSHP  2150
2151  TSPTAGQEPGPHPQGSGSVHGSPLLSTSGASTPGRGRRQLPQTPLTPRPS  2200
2201  VTYKTANSSPVHFAGAPSGLPAFSPGRLSRGLSEHNALLQRDPLSRPLAP  2250
2251  GSRIGSDPYLGQRLDSEAPARALPEDAPAFEETAASNSGRSSRTSYVSSL  2300
2301  TSQPPPLRRVPNGYHCTLGLGGGGRARRGCHHPDRDRRC             2339

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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