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

NucPred

Fetching O55017 from www.uniprot.org...

The NucPred score for your sequence is 0.68 (see score help below)

   1  MVRFGDELGGRYGGTGGGERARGGGAGGAGGPGQGGLPPGQRVLYKQSIA    50
  51  QRARTMALYNPIPVKQNCFTVNRSLFVFSEDNVVRKYAKRITEWPPFEYM   100
 101  ILATIIANCIVLALEQHLPDGDKTPMSERLDDTEPYFIGIFCFEAGIKII   150
 151  ALGFVFHKGSYLRNGWNVMDFVVVLTGILATAGTDFDLRTLRAVRVLRPL   200
 201  KLVSGIPSLQVVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYMGKFH   250
 251  KACFPNSTDTEPVGDFPCGKDPPARQCDGDTECREYWPGPNFGITNFDNI   300
 301  LFAILTVFQCITMEGWTDILYNTNDAAGNTWNWLYFIPLIIIGSFFMLNL   350
 351  VLGVLSGEFAKERERVENRRAFLKLRRQQQIERELNGYLEWIFKAEEVML   400
 401  AEEDKNAEEKSPLDVLKRAATKKSRNDLIHAEEGEDRFVDLCAVGSPFAR   450
 451  ASLKSGKTESSSYFRRKEKMFRFFIRRMVKAQSFYWVVLCVVALNTLCVA   500
 501  MVHYNQPQRLTTALYFAEFVFLGLFLTEMSLKMYGLGPRSYFRSSFNCFD   550
 551  FGVIVGSIFEVVWAAIKPGTSFGISVLRALRLLRIFKVTKYWNSLRNLVV   600
 601  SLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFQDETPTTNFDTFP   650
 651  AAILTVFQILTGEDWNAVMYHGIESQGGVSKGMFSSFYFIVLTLFGNYTL   700
 701  LNVFLAIAVDNLANAQELTKDEEEMEEAANQKLALQKAKEVAEVSPMSAA   750
 751  NISIAARQQNSAKARSVWEQRASQLRLQNLRASCEALYSEMDPEERLRYA   800
 801  STRHVRPDMKTHMDRPLVVEPGRDGLRGPVGSKSKPEGTEATESADLPRR   850
 851  HHRHRDRDKTSATAPAGGEQDRTESTETGAREERARPRRSHSKETPGADT   900
 901  QVRCERSRRHHRRGSPEEATEREPRRHRAHRHAQDSSKEGTAPVLVPKGE   950
 951  RRARHRGPRTGPREAENNEEPTRRHRARHKVPPTLQPPEREAAEKESNAV  1000
1001  EGDKETRNHQPKEPHCDLEAIAVTGVGPLHMLPSTCLQKVDEQPEDADNQ  1050
1051  RNVTRMGSQPSDPSTTVHVPVTLTGPPGETPVVPSGNMNLEGQAEGKKEA  1100
1101  EADDVLRRGPRPIVPYSSMFCLSPTNLLRRFCHYIVTMRYFEMVILVVIA  1150
1151  LSSIALAAEDPVRTDSFRNNALKYMDYIFTGVFTFEMVIKMIDLGLLLHP  1200
1201  GAYFRDLWNILDFIVVSGALVAFAFSSFMGGSKGKDINTIKSLRVLRVLR  1250
1251  PLKTIKRLPKLKAVFDCVVNSLKNVLNILIVYMLFMFIFAVIAVQLFKGK  1300
1301  FFYCTDESKELERDCRGQYLDYEKEEVEAQPRQWKKYDFHYDNVLWALLT  1350
1351  LFTVSTGEGWPMVLKHSVDATYEEQGPSPGFRMELSIFYVVYFVVFPFFF  1400
1401  VNIFVALIIITFQEQGDKVMSECSLEKNERACIDFAISAKPLTRYMPQNK  1450
1451  QSFQYKTWTFVVSPPFEYFIMAMIALNTVVLMMKFYDAPYEYELMLKCLN  1500
1501  IVFTSMFSMECILKIIAFGVLNYFRDAWNVFDFVTVLGSITDILVTEIAN  1550
1551  NFINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLLIAML  1600
1601  FFIYAIIGMQVFGNIALDDDTSINRHNNFRTFLQALMLLFRSATGEAWHE  1650
1651  IMLSCLGNRACDPHANASECGSDFAYFYFVSFIFLCSFLMLNLFVAVIMD  1700
1701  NFEYLTRDSSILGPHHLDEFIRVWAEYDPAACGRISYNDMFEMLKHMSPP  1750
1751  LGLGKKCPARVAYKRLVRMNMPISNEDMTVHFTSTLMALIRTALEIKLAP  1800
1801  AGTKQHQCDAELRKEISSVWANLPQKTLDLLVPPHKPDEMTVGKVYAALM  1850
1851  IFDFYKQNKTTRDQTHQAPGGLSQMGPVSLFHPLKATLEQTQPAVLRGAR  1900
1901  VFLRQKSATSLSNGGAIQTQESGIKESLSWGTQRTQDALYEARAPLERGH  1950
1951  SAEIPVGQSGTLAVDVQMQNMTLRGPDGEPQPGLESQGRAASMPRLAAET  2000
2001  QPAPNASPMKRSISTLAPRPHGTQLCSTVLDRPPPSQASHHHHHRCHRRR  2050
2051  DKKQRSLEKGPSLSVDPEGAPSTAAGPGLPHGEGSTACRRDRKQERGRSQ  2100
2101  ERRQPSSSSSEKQRFYSCDRFGSREPPQLMPSLSSHPTSPTAALEPAPHP  2150
2151  QGSGSVNGSPLMSTSGASTPGRGGRRQLPQTPLTPRPSITYKTANSSPVH  2200
2201  FAEGQSGLPAFSPGRLSRGLSEHNALLQKEPLSQPLAPGSRIGSDPYLGQ  2250
2251  RLDSEASAHTLPEDTLTFEEAVATNSGRSSRTSYVSSLTSQSHPLRRVPN  2300
2301  GYHCTLGLSTGVRARHSYHHPDQDHWC                         2327

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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