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

NucPred

Fetching P21951 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MMFGKKKNNGGSSTARYSAGNKYNTLSNNYALSAQQLLNASKIDDIDSMM    50
  51  GFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETLSSGSNGGG   100
 101  NSNDGERVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVN   150
 151  DVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLF   200
 201  EARKLLRPILQDNANNNVQRNIYNVAANGSEKVDAKHLIEDIREYDVPYH   250
 251  VRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKF   300
 301  PDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIF   350
 351  NENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFD   400
 401  EIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYN   450
 451  PIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTII   500
 501  PLNPDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLES   550
 551  ETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVEN   600
 601  KSSVDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMT   650
 651  TNRLQPDSIKAERDCASCDFNRPGKTCARKLKWAWRGEFFPSKMDEYNMI   700
 701  KRALQNETFPNKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRV   750
 751  KVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDP   800
 801  SDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGIT   850
 851  CLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKK   900
 901  LYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPY   950
 951  KAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQS  1000
1001  DIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENR  1050
1051  SMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNA  1100
1101  PVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERL  1150
1151  GSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIATKEDKFKQTSLTKFF  1200
1201  SKTKNVPTMGKIKDIEDLFEPTVEEDNAKIKIARTTKKKAVSKRKRNQLT  1250
1251  NEEDPLVLPSEIPSMDEDYVGWLNYQKIKWKIQARDRKRRDQLFGNTNSS  1300
1301  RERSALGSMIRKQAESYANSTWEVLQYKDSGEPGVLEVFVTINGKVQNIT  1350
1351  FHIPKTIYMKFKSQTMPLQKIKNCLIEKSSASLPNNPKTSNPAGGQLFKI  1400
1401  TLPESVFLEEKENCTSIFNDENVLGVFEGTITPHQRAIMDLGASVTFRSK  1450
1451  AMGALGKGIQQGFEMKDLSMAENERYLSGFSMDIGYLLHFPTSIGYEFFS  1500
1501  LFKSWGDTITILVLKPSNQAQEINASSLGQIYKQMFEKKKGKIETYSYLV  1550
1551  DIKEDINFEFVYFTDISKLYRRLSQETTKLKEERGLQFLLLLQSPFITKL  1600
1601  LGTIRLLNQMPIVKLSLNEVLLPQLNWQPTLLKKLVNHVLSSGSWISHLI  1650
1651  KLSQYSNIPICNLRLDSMDYIIDVLYARKLKKENIVLWWNEKAPLPDHGG  1700
1701  IQNDFDLNTSWIMNDSEFPKINNSGVYDNVVLDVGVDNLTVNTILTSALI  1750
1751  NDAEGSDLVNNNMGIDDKDAVINSPSEFVHDAFSNDALNVLRGMLKEWWD  1800
1801  EALKENSTADLLVNSLASWVQNPNAKLFDGLLRYHVHNLTKKALLQLVNE  1850
1851  FSALGSTIVYADRNQILIKTNKYSPENCYAYSQYMMKAVRTNPMFSYLDL  1900
1901  NIKRYWDLLIWMDKFNFSGLACIEIEEKENQDYTAVSQWQLKKFLSPIYQ  1950
1951  PEFEDWMMIILDSMLKTKQSYLKLNSGTQRPTQIVNVKKQDKEDSVENSL  2000
2001  NGFSHLFSKPLMKRVKKLFKNQQEFILDPQYEADYVIPVLPGSHLNVKNP  2050
2051  LLELVKSLCHVMLLSKSTILEIRTLRKELLKIFELREFAKVAEFKDPSLS  2100
2101  LVVPDFLCEYCFFISDIDFCKAAPESIFSCVRCHKAFNQVLLQEHLIQKL  2150
2151  RSDIESYLIQDLRCSRCHKVKRDYMSAHCPCAGAWEGTLPRESIVQKLNV  2200
2201  FKQVAKYYGFDILLSCIADLTI                              2222

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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