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

NucPred

Fetching Q7PPA5 from www.uniprot.org...

The NucPred score for your sequence is 0.07 (see score help below)

   1  MEDGHSKTVDEVLSHFRVDPERGLSLDQVKEYQKKYGPNELPAEEGKTLW    50
  51  QLVLEQFDDLLVKILLLAAIISFVLALFEEHEGVEAFVEPFVILLILIAN   100
 101  AVVGVWQERNAESAIEALKEYEPEMGKVIRGDKSGVQKIRAKEIVPGDVV   150
 151  EVSVGDKIPADIRLIKIYSTTIRIDQSILTGESVSVIKHTDAVPDPRAVN   200
 201  QDKKNILFSGTNVAAGKARGVVIGTGLNTAIGKIRTEMSETEEIKTPLQQ   250
 251  KLDEFGEQLSKVISLICVAVWAINIGHFNDPAHGGSWIKGAVYYFKIAVA   300
 301  LAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSD   350
 351  KTGTLTTNQMSVSRMFIFEKIEGNDSSFTEFEISGSTYEPIGEVTLNGQR   400
 401  IKAADYETLHELGTICIMCNDSAIDFNETKKVFEKVGEATETALIVLAEK   450
 451  LNPFNVAKQGLDRRSSAICVRQEIETKWKKEFTLEFSRDRKSMSSYCTPL   500
 501  KASKLGNGPKLFCKGAPEGVLERCTHARVGSTKVPLTQTLKQRILDLTRT   550
 551  YGTGRDTLRCLALATADSPMKPDDMDLNDSTKFYTYEVNLTFVGVVGMLD   600
 601  PPRKEVQDSIVRCRAAGIRVIVITGDNKATAEAICRRIGVFGEDEDTTGK   650
 651  SYSGREFDDLSVSEQREACSRARLFSRVEPAHKSKIVEFLQSMNEISAMT   700
 701  GDGVNDAPALKKAEIGIAMGSGTAVAKSAAEMVLADDNFSSIVAAVEEGR   750
 751  AIYNNMKQFIRYLISSNIGEVVSIFLTAALGLPEALIPVQLLWVNLVTDG   800
 801  LPATALGFNPPDLDIMTKPPRKADEGLISGWLFFRYMAIGGYVGCATVGG   850
 851  AAWWFMFSETGPQLSYWQLTHHLSCLGGGEEFKGIDCKIFNDPHPMTMAL   900
 901  SVLVTIEMLNAMNSLSENQSLVQMPPWCNIWLIASMCLSFALHFVILYVD   950
 951  VLSTVFQVTPLDGNEWMTVMKFSLPVVLLDEILKFVARRISDGESYIKNM  1000
1001  HGLVLAWAVFFAYIIWGP                                  1018

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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