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

NucPred

Fetching Q9Y618 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MSGSTQPVAQTWRATEPRYPPHSLSYPVQIARTHTDVGLLEYQHHSRDYA    50
  51  SHLSPGSIIQPQRRRPSLLSEFQPGNERSQELHLRPESHSYLPELGKSEM   100
 101  EFIESKRPRLELLPDPLLRPSPLLATGQPAGSEDLTKDRSLTGKLEPVSP   150
 151  PSPPHTDPELELVPPRLSKEELIQNMDRVDREITMVEQQISKLKKKQQQL   200
 201  EEEAAKPPEPEKPVSPPPIESKHRSLVQIIYDENRKKAEAAHRILEGLGP   250
 251  QVELPLYNQPSDTRQYHENIKINQAMRKKLILYFKRRNHARKQWEQKFCQ   300
 301  RYDQLMEAWEKKVERIENNPRRRAKESKVREYYEKQFPEIRKQRELQERM   350
 351  QSRVGQRGSGLSMSAARSEHEVSEIIDGLSEQENLEKQMRQLAVIPPMLY   400
 401  DADQQRIKFINMNGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKN   450
 451  FGLIASFLERKTVAECVLYYYLTKKNENYKSLVRRSYRRRGKSQQQQQQQ   500
 501  QQQQQQQQQQPMPRSSQEEKDEKEKEKEAEKEEEKPEVENDKEDLLKEKT   550
 551  DDTSGEDNDEKEAVASKGRKTANSQGRRKGRITRSMANEANSEEAITPQQ   600
 601  SAELASMELNESSRWTEEEMETAKKGLLEHGRNWSAIARMVGSKTVSQCK   650
 651  NFYFNYKKRQNLDEILQQHKLKMEKERNARRKKKKAPAAASEEAAFPPVV   700
 701  EDEEMEASGVSGNEEEMVEEAEALHASGNEVPRGECSGPATVNNSSDTES   750
 751  IPSPHTEAAKDTGQNGPKPPATLGADGPPPGPPTPPPEDIPAPTEPTPAS   800
 801  EATGAPTPPPAPPSPSAPPPVVPKEEKEEETAAAPPVEEGEEQKPPAAEE   850
 851  LAVDTGKAEEPVKSECTEEAEEGPAKGKDAEAAEATAEGALKAEKKEGGS   900
 901  GRATTAKSSGAPQDSDSSATCSADEVDEAEGGDKNRLLSPRPSLLTPTGD   950
 951  PRANASPQKPLDLKQLKQRAAAIPPIQVTKVHEPPREDAAPTKPAPPAPP  1000
1001  PPQNLQPESDAPQQPGSSPRGKSRSPAPPADKEAFAAEAQKLPGDPPCWT  1050
1051  SGLPFPVPPREVIKASPHAPDPSAFSYAPPGHPLPLGLHDTARPVLPRPP  1100
1101  TISNPPPLISSAKHPSVLERQIGAISQGMSVQLHVPYSEHAKAPVGPVTM  1150
1151  GLPLPMDPKKLAPFSGVKQEQLSPRGQAGPPESLGVPTAQEASVLRGTAL  1200
1201  GSVPGGSITKGIPSTRVPSDSAITYRGSITHGTPADVLYKGTITRIIGED  1250
1251  SPSRLDRGREDSLPKGHVIYEGKKGHVLSYEGGMSVTQCSKEDGRSSSGP  1300
1301  PHETAAPKRTYDMMEGRVGRAISSASIEGLMGRAIPPERHSPHHLKEQHH  1350
1351  IRGSITQGIPRSYVEAQEDYLRREAKLLKREGTPPPPPPSRDLTEAYKTQ  1400
1401  ALGPLKLKPAHEGLVATVKEAGRSIHEIPREELRHTPELPLAPRPLKEGS  1450
1451  ITQGTPLKYDTGASTTGSKKHDVRSLIGSPGRTFPPVHPLDVMADARALE  1500
1501  RACYEESLKSRPGTASSSGGSIARGAPVIVPELGKPRQSPLTYEDHGAPF  1550
1551  AGHLPRGSPVTTREPTPRLQEGSLSSSKASQDRKLTSTPREIAKSPHSTV  1600
1601  PEHHPHPISPYEHLLRGVSGVDLYRSHIPLAFDPTSIPRGIPLDAAAAYY  1650
1651  LPRHLAPNPTYPHLYPPYLIRGYPDTAALENRQTIINDYITSQQMHHNAA  1700
1701  TAMAQRADMLRGLSPRESSLALNYAAGPRGIIDLSQVPHLPVLVPPTPGT  1750
1751  PATAMDRLAYLPTAPQPFSSRHSSSPLSPGGPTHLTKPTTTSSSERERDR  1800
1801  DRERDRDREREKSILTSTTTVEHAPIWRPGTEQSSGSSGGGGGSSSRPAS  1850
1851  HSHAHQHSPISPRTQDALQQRPSVLHNTGMKGIITAVEPSTPTVLRSTST  1900
1901  SSPVRPAATFPPATHCPLGGTLDGVYPTLMEPVLLPKEAPRVARPERPRA  1950
1951  DTGHAFLAKPPARSGLEPASSPSKGSEPRPLVPPVSGHATIARTPAKNLA  2000
2001  PHHASPDPPAPPASASDPHREKTQSKPFSIQELELRSLGYHGSSYSPEGV  2050
2051  EPVSPVSSPSLTHDKGLPKHLEELDKSHLEGELRPKQPGPVKLGGEAAHL  2100
2101  PHLRPLPESQPSSSPLLQTAPGVKGHQRVVTLAQHISEVITQDYTRHHPQ  2150
2151  QLSAPLPAPLYSFPGASCPVLDLRRPPSDLYLPPPDHGAPARGSPHSEGG  2200
2201  KRSPEPNKTSVLGGGEDGIEPVSPPEGMTEPGHSRSAVYPLLYRDGEQTE  2250
2251  PSRMGSKSPGNTSQPPAFFSKLTESNSAMVKSKKQEINKKLNTHNRNEPE  2300
2301  YNISQPGTEIFNMPAITGTGLMTYRSQAVQEHASTNMGLEAIIRKALMGK  2350
2351  YDQWEESPPLSANAFNPLNASASLPAAMPITAADGRSDHTLTSPGGGGKA  2400
2401  KVSGRPSSRKAKSPAPGLASGDRPPSVSSVHSEGDCNRRTPLTNRVWEDR  2450
2451  PSSAGSTPFPYNPLIMRLQAGVMASPPPPGLPAGSGPLAGPHHAWDEEPK  2500
2501  PLLCSQYETLSDSE                                      2514

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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