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

NucPred

Fetching Q28343 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MTTLLWVFVTLRVITAASSEETSDHDNSLSVSIPEPSPMRVLLGSSLTIP    50
  51  CYFIDPMHPVTTAPSTAPLAPRIKWSRITKEKEVVLLVATEGQVRINSAY   100
 101  QDKVSLPNYPAIPSDATLEIQNLRSNDSGIYRCEVMHGIEDSEATLEVVV   150
 151  KGIVFHYRAISTRYTLDFDRAQRACLQNSAIIATPEQLQAAYEDGFHQCD   200
 201  AGWLADQTVRYPIHTPREGCYGDKDEFPGVRTYGIRDTNETYDVYCFAEE   250
 251  MEGEVLYATSPEKFTFQEAANECRRLGARLATTGQLYLAWQGGMDMCSAG   300
 301  WLADRSVRYPISKARPNCGGNLLGVRTVYLHANQTGYPDPSSRYDAICYT   350
 351  GEDFVDIPENFFGVGGEEDITIQTVTWPDVELPLPRNITEGEARGNVILT   400
 401  VKPIFDLSPTAPEPEEPFTFVPEPEKPFTFATDVGVTAFPEAENRTGEAT   450
 451  RPWGVPEESTPGPAFTAFTSEDHVVQVTAVPGAAEVPGQPRLPGGVVFHY   500
 501  RPGSARYSLTFEEAQQACLRTGAVIASPEQLQAAYEAGYEQCDAGWLQDQ   550
 551  TVRYPIVSPRTPCVGDKDSSPGVRTYGVRPPSETYDVYCYVDKLEGEVFF   600
 601  ITRLEQFTFQEALAFCESHNATLASTGQLYAAWRQGLDKCYAGWLSDGSL   650
 651  RYPIVTPRPSCGGDKPGVRTVYLYPNQTGLPDPLSRHHVFCFRGVSGVPS   700
 701  PGEEEGGTPTPSVVEDWIPTQVGPVVPSVPMGEETTAILDFTIEPENQTE   750
 751  WEPAYSPAGTSPLPGIPPTWPPTSTATEESTEGPSGTEVPSVSEEPSPSE   800
 801  EPFPWEELSTLSPPGPSGTELPGSGEASGVPEVSGDFTGSGEVSGHPDSS   850
 851  GQLSGESASGLPSEDLDSSGLTSAVGSGLASGDEDRITLSSIPKVEGEGL   900
 901  ETSASGVEDLSGLPSGREGLETSTSGVGDLSGLPSGEGLEVSASGVEDLS   950
 951  GLPSGEGPETSTSGVGDLSRLPSGEGPEVSASGVGDLSGLPSGREGLETS  1000
1001  TSGVEDLSGLPSGEGPEASTSGVGDLSRLPSGEGPEVSASGVEDLSGLPS  1050
1051  GEGLEASASGVGDLSGLPSGEGPEASASGVGDLSRLPSGEGPEVSASGVE  1100
1101  DLSGLSSGESPEASASGVGDLSGLPSGREGLETSASGVGDLSGLPSGEGQ  1150
1151  EASASGVEDLSRLPSGEGPEASASGVGELSGLPSGREGLETSASGVGDLS  1200
1201  GLPSGEGPEAFASGVEDLSILPSGEGPEASASGVGDLSGLPSGREGLETS  1250
1251  TSGVGDLSGLPSGREGLETSTSGVGDLSGLPSGEGPEASASGIGDISGLP  1300
1301  SGREGLETSSSGVEDHPETSASGVEDLSGLPSGVEGHPETSASGVEDLSD  1350
1351  LSSGGEGLETSASGAEDLSGFPSGKEDLIGSASGALDFGRIPSGTLGSGQ  1400
1401  APEASSLPSGFSGEYSGVDFGSGPISGLPDFSGLPSGFPTISLVDTTLVE  1450
1451  VITTTSASELEGRGTIGISGAGETSGLPVSELDISGAVSGLPSGAELSGQ  1500
1501  ASGSPDMSGETSGFFGVSGQPSGFPDISGGTSGLFEVSGQPSGFSGETSG  1550
1551  VTELSGLYSGQPDVSGEASGVPSGSGQPFGMTDLSGETSGVPDISGQPSG  1600
1601  LPEFSGTTSGIPDLVSSTMSGSGESSGITFVDTSLVEVTPTTFKEKKRLG  1650
1651  SVELSGLPSGEVDLSGASGTMDISGQSSGATDSSGLTSHLPKFSGLPSGA  1700
1701  AEVSGESSGAEVGSSLPSGTYEGSGNFHPAFPTVFLVDRTLVESVTQAPT  1750
1751  AQEAGEGPSGILELSGAHSGAPDVSGDHSGSLDLSGMQSGLVEPSGEPSS  1800
1801  TPYFSGDFSGTMDVTGEPSTAMSASGEASGLLEVTLITSEFVEGVTEPTV  1850
1851  SQELAQRPPVTHTPQLFESSGEASASGEISGATPAFPGSGLEASSVPESS  1900
1901  SETSDFPERAVGVSAAPEASGGASGAPDVSEATSTFPEADVEGASGLGVS  1950
1951  GGTSAFPEAPREGSATPEVQEEPTTSYDVGREALGWPSATPTASGDRIEV  2000
2001  SGDLSGHTSGLDVVISTSVPESEWIQQTQRPAEAHLEIEASSPLHSGEET  2050
2051  QTAETATSPTDDASIPTSPSGTDESAPAIPDIDECLSSPCLNGATCVDAI  2100
2101  DSFTCLCLPSYRGDLCEIDQELCEEGWTKFQGHCYRYFPDRESWVDAESR  2150
2151  CRAQQSHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHSLQ  2200
2201  FENWRPNQPDNFFVSGEDCVVMIWHEKGEWNDVPCNYYLPFTCKKGTVAC  2250
2251  GDPPVVEHARTFGQKKDRYEINSLVRYQCTEGFVQRHVPTIRCQPSGHWE  2300
2301  KPRITCTDPSTYKRRLQKRSSRAPRRSRPSTAH                   2333

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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