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

NucPred

Fetching Q4PFV5 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MPSTFGLTSRASNVRSRGTFRKRGGGPRSGSFKSATEKAIANAAAQLVKG    50
  51  VEDGSAVEERFQELKERDEIDEKLGFHRLEQGQTRQAWLVNMHPTLLRDP   100
 101  DHPTGKSGVDFYFIEDDASMFKATVLYQPYFLVGCRPGTESSVEEWLRRR   150
 151  YEGLVQSIQRDRKEDLKLPNHLLGNQRLYLRLTFLNVQDLLSVRKELLPI   200
 201  AKAAQKKLSAVDTYADVLSAASAAASASLGIQLDSDGHNAALDPDDGWTG   250
 251  ARKRAAASALDPAECLVDIREYDIPYYLRVAIDQDVRVGLWYDVSFEDGI   300
 301  VSLNMVKDRVKRADPVVMAFDIETTKQPLKFPDAETDAVMMISYMIDGQG   350
 351  FLITNREIVSEDIEDFEYTPRDEYEGPFIIFNEPDELGVLQRFFSHFREA   400
 401  RPTVVATYNGDLFDFPFIDARARAHGLNMMSEIGFAKDSDNEYKSRATAH   450
 451  LDCFRWVQRDSYLPQGSQGLKAVTVAKLGYDPMELDPELMTPYAIEQPQT   500
 501  LAQYSVSDAVATYYLYMKYVHPFIFSLCNIIPLNPDEVLRKGSGTLCETL   550
 551  LMVQAFKGNIIMPNRHEDPVGNTYKGHLLESETYVGGHVEALEAGVFRSD   600
 601  IETDFRVDPAAIQQLIDDLDAALQFSIREEGKLDLDDIENYDEVKAEIRT   650
 651  MLEVMRDQPVRKDCPLIYHLDVAAMYPNIMLSYRLQPDSMVSEAMCATCD   700
 701  YNRPGMKCDKRMDWAWRGEYFPAKRDEVNMIRNALSNETFPPKAAHLARR   750
 751  TYDDLDPNERTALLHKRLGDYSRKVYRKTHESKTVIREAVICQRENPFYI   800
 801  NTVRDFRDRRYEYKGLHKTWKKNLDKADSLNDTIEAKKMIVLYDSLQLAH   850
 851  KCILNSFYGYVMRKGARWYSMEMAGITCLTGASIIQMAKELVDRIGRPLE   900
 901  LDTDGIWCMLPGVFPENFNFKVKGGKKFGISYPCTMLNHLVHEKFTNHQY   950
 951  HELVDKQTGKYEVRSENSIFFELDGPYKAMILPSSKEEDKLLKKRYAVFN  1000
1001  TDGSLAELKGFEVKRRGELQLIKDFQKQIFEKFLLGTTLNECYAAVAKVA  1050
1051  NQWLDVLYSKGSTLHDEELIDLIAENKSMSKTLQEYGSLKSTAITTAKRL  1100
1101  AEFLGAQMIKDKGLACKFIISAKPFGAPVTERAVPVALFNAEPSVKHYYL  1150
1151  KKFLRDNSITDFDIRNILDWNYYIERFGGVIQKLITIPAAMQKVSNPVPR  1200
1201  VRHPDWLHKRVAAREDKFKQRKLTDVFRPAAKPTSIEACTTLKPAAAVAS  1250
1251  ADIVENEPEVEEVAPDITVDYSGWVAVMKKKWRKQRLQRAKERKARANGG  1300
1301  GAFISSSLGKGTVGSMFSKRSANMATAVWDIVQICATSRPGEYRLWISID  1350
1351  QHLQSLKLKVPRQFYVNFKSQPSESVFLSGVYRAERLVKTLPRDAPCRHL  1400
1401  YRITVDEDVYQEQESHFSNLIHHPNVEGVYEKQLPLDVRALIQLGSTCVY  1450
1451  GRNSQAPKLSRALDTGFHLQDLSAPTSVDISPNHKYLSGGAGIRYFYLYH  1500
1501  AHRDGRHVISLFSPEGEIKMHIVDSAGLRQVPNVETMYADRVAHMRKRGK  1550
1551  LEEGSGVFEYSDTMRVDVRVHTSTTRAFKAITKELGSLKAAKQGSAMLAL  1600
1601  CTSKDQAYYESHIPSVAEFPIIKIAAAALEDELPALGWQLYSARRMLQCY  1650
1651  LRASNWIRGWIDLASHFDLPLCNMEKDFTIFGADIDFARRLVKQDMVLWW  1700
1701  SPHPRPDLGGREQDIHAQSRWDEQESLEISHAGAYSTVCLEVGLVDLAVD  1750
1751  SVLQSGSVNEMEGSTSGFAFEGASHNLDEYSRGTVETATILGDSVLTSAV  1800
1801  FAAVKGMVKAWYTTKRRNRSPYAALLSDNFWRWASSDGSALFEPALQRFL  1850
1851  FGLMKKTLLQLLAEFKRLGASIVYASFNRLFLLTSKPTAANAMAYSRYLL  1900
1901  TAVTSRELFKHVQLDIIHYWEYLLWMDTANFGGVIADTDSLVAPTDEQAQ  1950
1951  EASAANQVATFNVEMNWNIQTFLPLAVQEKFSVAVGSFIYSLYEYKRRAA  2000
2001  LAGEHERTPLRAVVEPNTPADPVTLHGDGGQVNGDGGKDDRTALAPAAKF  2050
2051  TSDLINHTMTRKLLKHLSELKSSMQTSSDEINAAIARDEDEEYIDMLTTE  2100
2101  HRRMWSFPVLPGSWLTPSNPLLEFIKTTNAVLSLAKDHAIEVSILKRNLL  2150
2151  DMIKVREFSPEAEFRNPCEPFKLPLVICTFCNDDRTLDLCRDADLMPSAA  2200
2201  SNGGGAPKWKCAKCQFPYNIAALEMRLVNTANAYLESFHLQDLRCNKCGA  2250
2251  LKQTNLQPHCECSGSFGLMVTRKETLKRLKSLKTIAEFHGLETTAMAVES  2300
2301  MLAMV                                               2305

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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