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

NucPred

Fetching P26019 from www.uniprot.org...

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

   1  MSESPSEPRAKRQRVDKNGRFAAMERLRQLKGTKNKCKVEDQVDDVYDVV    50
  51  DEREYAKRAQEKYGDDWIEEDGTGYAEDLRDFFEDEDEYSDGEEDRKDSK   100
 101  KKKGVAPNSKKRPRENEKPVTGKASIKNLFSNAVPKKMDVKTSVKDDDIL   150
 151  ADILGEIKEEPAATSEKAEKVIAPAKISVTSRKFDAAAAKEYMNSFLNNI   200
 201  KVQEQERKKAEASSDNEMLERILKPKAAVPNTKVAFFSSPTIKKEPMPEK   250
 251  TPAKKATEDPFSDNEMDFSCLDDDENQFDVEKTQQTEKVSQTKTAAEKTS   300
 301  QSKVAEKSAPKKETTGSPKESESEDISRLLNNWESICQMDDDFEKSVLTT   350
 351  EQDSTISSDQQLRFWYWEAYEDPVKMPGEVFLFGRTADGKSVCLRVQNIN   400
 401  RVLYLLPRQFLLDPISKEPTKQKVTVADIYKEFDSEVANQLKLEFFRSRK   450
 451  VTKSFAHHAIGIEVPQSCDYLEVHYDGKKPLPNLSADKKYNSIAHIFGAT   500
 501  TNALERFLLDRKIKGPCWLQVTGFKVSPTPMSWCNTEVTLTEPKNVELVQ   550
 551  DKGKPAPPPPLTLLSLNVRTSMNPKTSRNEICMISMLTHNRFHIDRPAPQ   600
 601  PAFNRHMCALTRPAVVSWPLDLNFEMAKYKSTTVHKHDSERALLSWFLAQ   650
 651  YQKIDADLIVTFDSMDCQLNVITDQIVALKIPQWSRMGRLRLSQSFGKRL   700
 701  LEHFVGRMVCDVKRSAEECIRARSYDLQTLCKQVLKLKESERMEVNADDL   750
 751  LEMYEKGESITKLISLTMQDNSYLLRLMCELNIMPLALQITNICGNTMTR   800
 801  TLQGGRSERNEFLLLHAFHEKNYIVPDKKPVSKRSGAGDTDATLSGADAT   850
 851  MQTKKKAAYAGGLVLEPMRGLYEKYVLLMDFNSLYPSIIQEYNICFTTVQ   900
 901  QPVDADELPTLPDSKTEPGILPLQLKRLVESRKEVKKLMAAPDLSPELQM   950
 951  QYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKGREILTNTQQL  1000
1001  VQKMNYDVVYGDTDSLMINTNITDYDQVYKIGHNIKQSVNKLYKQLELDI  1050
1051  DGVFGCLLLLKKKKYAAIKLSKDSKGNLRREQEHKGLDIVRRDWSQLAVM  1100
1101  VGKAVLDEVLSEKPLEEKLDAVHAQLEKIKTQIAEGVVPLPLFVITKQLT  1150
1151  RTPQEYANSASLPHVQVALRMNRERNRRYKKGDMVDYVICLDGTTNAAMQ  1200
1201  RAYHLDELKTSEDKKLQLDTNYYLGHQIHPVVTRMVEVLEGTDASRIAEC  1250
1251  LGMDPTKFRQNAQRTQRENTEQSEGESLLKTTLQLYRLCEPFRFQCVTCK  1300
1301  TEQLMASAYRPGPSNSHIAVLQQCAKSECQTAPIQYLASVRNQLQLSMRQ  1350
1351  YVQRFYKNWLVCDHPDCNFNTRTHSLRKKSHRPLCQKCRSGSLLRQYTER  1400
1401  DLYNQLCYLRFMFDLGKQTLQQKPTLTPELEQAYQLLYETVDQQLQSSSY  1450
1451  VIISLSKLFARSLAQMSLQPSVAQPQIEAIPSALADVV              1488

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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