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

NucPred

Fetching O75376 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSSSGYPPNQGAFSTEQSRYPPHSVQYTFPNTRHQQEFAVPDYRSSHLEV    50
  51  SQASQLLQQQQQQQLRRRPSLLSEFHPGSDRPQERRTSYEPFHPGPSPVD   100
 101  HDSLESKRPRLEQVSDSHFQRVSAAVLPLVHPLPEGLRASADAKKDPAFG   150
 151  GKHEAPSSPISGQPCGDDQNASPSKLSKEELIQSMDRVDREIAKVEQQIL   200
 201  KLKKKQQQLEEEAAKPPEPEKPVSPPPVEQKHRSIVQIIYDENRKKAEEA   250
 251  HKIFEGLGPKVELPLYNQPSDTKVYHENIKTNQVMRKKLILFFKRRNHAR   300
 301  KQREQKICQRYDQLMEAWEKKVDRIENNPRRKAKESKTREYYEKQFPEIR   350
 351  KQREQQERFQRVGQRGAGLSATIARSEHEISEIIDGLSEQENNEKQMRQL   400
 401  SVIPPMMFDAEQRRVKFINMNGLMEDPMKVYKDRQFMNVWTDHEKEIFKD   450
 451  KFIQHPKNFGLIASYLERKSVPDCVLYYYLTKKNENYKALVRRNYGKRRG   500
 501  RNQQIARPSQEEKVEEKEEDKAEKTEKKEEEKKDEEEKDEKEDSKENTKE   550
 551  KDKIDGTAEETEEREQATPRGRKTANSQGRRKGRITRSMTNEAAAASAAA   600
 601  AAATEEPPPPLPPPPEPISTEPVETSRWTEEEMEVAKKGLVEHGRNWAAI   650
 651  AKMVGTKSEAQCKNFYFNYKRRHNLDNLLQQHKQKTSRKPREERDVSQCE   700
 701  SVASTVSAQEDEDIEASNEEENPEDSEVEAVKPSEDSPENATSRGNTEPA   750
 751  VELEPTTETAPSTSPSLAVPSTKPAEDESVETQVNDSISAETAEQMDVDQ   800
 801  QEHSAEEGSVCDPPPATKADSVDVEVRVPENHASKVEGDNTKERDLDRAS   850
 851  EKVEPRDEDLVVAQQINAQRPEPQSDNDSSATCSADEDVDGEPERQRMFP   900
 901  MDSKPSLLNPTGSILVSSPLKPNPLDLPQLQHRAAVIPPMVSCTPCNIPI   950
 951  GTPVSGYALYQRHIKAMHESALLEEQRQRQEQIDLECRSSTSPCGTSKSP  1000
1001  NREWEVLQPAPHQVITNLPEGVRLPTTRPTRPPPPLIPSSKTTVASEKPS  1050
1051  FIMGGSISQGTPGTYLTSHNQASYTQETPKPSVGSISLGLPRQQESAKSA  1100
1101  TLPYIKQEEFSPRSQNSQPEGLLVRAQHEGVVRGTAGAIQEGSITRGTPT  1150
1151  SKISVESIPSLRGSITQGTPALPQTGIPTEALVKGSISRMPIEDSSPEKG  1200
1201  REEAASKGHVIYEGKSGHILSYDNIKNAREGTRSPRTAHEISLKRSYESV  1250
1251  EGNIKQGMSMRESPVSAPLEGLICRALPRGSPHSDLKERTVLSGSIMQGT  1300
1301  PRATTESFEDGLKYPKQIKRESPPIRAFEGAITKGKPYDGITTIKEMGRS  1350
1351  IHEIPRQDILTQESRKTPEVVQSTRPIIEGSISQGTPIKFDNNSGQSAIK  1400
1401  HNVKSLITGPSKLSRGMPPLEIVPENIKVVERGKYEDVKAGETVRSRHTS  1450
1451  VVSSGPSVLRSTLHEAPKAQLSPGIYDDTSARRTPVSYQNTMSRGSPMMN  1500
1501  RTSDVTISSNKSTNHERKSTLTPTQRESIPAKSPVPGVDPVVSHSPFDPH  1550
1551  HRGSTAGEVYRSHLPTHLDPAMPFHRALDPAAAAYLFQRQLSPTPGYPSQ  1600
1601  YQLYAMENTRQTILNDYITSQQMQVNLRPDVARGLSPREQPLGLPYPATR  1650
1651  GIIDLTNMPPTILVPHPGGTSTPPMDRITYIPGTQITFPPRPYNSASMSP  1700
1701  GHPTHLAAAASAEREREREREKERERERIAAASSDLYLRPGSEQPGRPGS  1750
1751  HGYVRSPSPSVRTQETMLQQRPSVFQGTNGTSVITPLDPTAQLRIMPLPA  1800
1801  GGPSISQGLPASRYNTAADALAALVDAAASAPQMDVSKTKESKHEAARLE  1850
1851  ENLRSRSAAVSEQQQLEQKTLEVEKRSVQCLYTSSAFPSGKPQPHSSVVY  1900
1901  SEAGKDKGPPPKSRYEEELRTRGKTTITAANFIDVIITRQIASDKDARER  1950
1951  GSQSSDSSSSLSSHRYETPSDAIEVISPASSPAPPQEKLQTYQPEVVKAN  2000
2001  QAENDPTRQYEGPLHHYRPQQESPSPQQQLPPSSQAEGMGQVPRTHRLIT  2050
2051  LADHICQIITQDFARNQVSSQTPQQPPTSTFQNSPSALVSTPVRTKTSNR  2100
2101  YSPESQAQSVHHQRPGSRVSPENLVDKSRGSRPGKSPERSHVSSEPYEPI  2150
2151  SPPQVPVVHEKQDSLLLLSQRGAEPAEQRNDARSPGSISYLPSFFTKLEN  2200
2201  TSPMVKSKKQEIFRKLNSSGGGDSDMAAAQPGTEIFNLPAVTTSGSVSSR  2250
2251  GHSFADPASNLGLEDIIRKALMGSFDDKVEDHGVVMSQPMGVVPGTANTS  2300
2301  VVTSGETRREEGDPSPHSGGVCKPKLISKSNSRKSKSPIPGQGYLGTERP  2350
2351  SSVSSVHSEGDYHRQTPGWAWEDRPSSTGSTQFPYNPLTMRMLSSTPPTP  2400
2401  IACAPSAVNQAAPHQQNRIWEREPAPLLSAQYETLSDSDD            2440

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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