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

NucPred

Fetching Q05973 from www.uniprot.org...

The NucPred score for your sequence is 0.28 (see score help below)

   1  MDEKYTAKNRDKTFVVIEKRFKKNIIHRFSAKRSLFLFTPRNPIRRLAVC    50
  51  IATNVCFDYFLMFTIMINCVFLAMPDISEFAEYIFLGIYTMEMAIKLVAG   100
 101  GFFIDKYTYLRDAWNCLDFTVIMISYITLLLQTINDKVISDITGLRTFRV   150
 151  LRALRTLSIIPGLKTMVNALLRALRMLISVLILILFCLWIFSQAGVQLFG   200
 201  GALRHKCVLQIHGSPAFGKTYDEFYAEHIENSDNWLAKGNGEYVLCGNAT   250
 251  GAGPCPTNYTCLPDIGENPNYGYTNFDSIGWSMLISFQLLTQDYWEDVYN   300
 301  KVIRAHSPWTVIYFIVINFFGSLYLMNLMLAVVATAYELEVKNTGKKLQQ   350
 351  TAATAREQSLKEQERRNTLTVSEADSHVDDRNCTCCEQCCGCCYNPWLRV   400
 401  QSFAHCIITDSFTEVFIIFIIVLNTVFLAMEHHGMSMELKNVLKVANYVF   450
 451  TTVFVLEAILKLLAFNKQYFKSGWNICDLVVVVASLIDLGVEGLKGVSVF   500
 501  RSFRLLRVFHLAQSWTTMRLLLCIILNTLGSLGYLTIILIIVIYIFAVTG   550
 551  LQLFHTEYTPDKFRGEPVPRWNFNDFLHSFMMVFRILCGEWIEPMYDCMR   600
 601  ACNGLCFLIFIPVTVFGKTLFFLFIGLVLGAFGSDTVEQEVEVSSFALPG   650
 651  PESKPCSVRERGISATDDNVKDDGQDEVQQNSEETKIDLRNNDKQSKDGM   700
 701  ILENNCNNDSLASLGSLGSIPDIMDGSSVEDDISSCQQKDIQPCLPLFIS   750
 751  SRFKCLREFDDTSHGKKWNNFRRQLMMVCENKYFETGVLVIIFASSILLA   800
 801  FEDIYLNEKPRLKLAIFYLDITFCLLFFLEMVLKLVALGFVHYYTHFWTI   850
 851  LDFTIVIITVISLAASGLGMEQITAFRSLRTLRALRPLRAVSRWQGMKII   900
 901  VNALMLSIPSIFNVLLVCVVFWLIFAIMGVQLFAGKFYKCVNETNMRIPP   950
 951  TEVANKIECYNKNYTWVNSNVNFDNVGGAFLALFQVATFEGWMEIMADAV  1000
1001  DVTEVDEQPKFEATVYYYFYFVLFIIFGSFFVLNLVIGVIIDKFSFLKKK  1050
1051  YDGTYLDMFLTPTQQNYYNTLKKLGTKKPQKTVKRPKNKCQAVVYDLVMS  1100
1101  NQFEIFITTIIITNMIFMAFEHYNQSEVVTEVLATANIAFTILYAVEAII  1150
1151  KIIGLRIHYLRNLWNVFDFLVVTLSVMDAFLNDIFGDGIFMNPSLLRVAR  1200
1201  MFRIGRIIRLIKWAKGMRKLLFALVISLPALFNIGALLMLVMFIYTIIGM  1250
1251  SSFGQIKLSGALNDQVNFQTFGKTFLLLVRLATSAGWNDILGPLLIQPPN  1300
1301  CDPNYITTSTGEKIKVVNGDCGMPWLAISYMVSYIIIVFMIVFNMYIAVI  1350
1351  LENFNQAHAQEEVGITEDDLDMFYGVWEQYDPLATQFIKHEQLSDFIQDL  1400
1401  DPPLKVKKPNNVAIATFDLPIVKGGHIHCLDILLALVKFALGGNLEETEA  1450
1451  FKRVRTQMEARFDEIFPTREKSEIRTSTLQMRREEMAARTLQRAWKRRKI  1500
1501  MRSFPSPEMIRYFIISAPETAV                              1522

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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