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

NucPred

Fetching Q9UTJ8 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MSCIDRMSIMGIRSFDNRSRESIQFFSPLTLIVGQNGSGKTTIIECLKYA    50
  51  TTGILPPNTKGGAFIHDPKICGEKEVLAQVKLAFRNTNQVKMICTRSLQL   100
 101  SVKKTTRQQKTLDGQLLILKDNERTTISNRCAELDSQVPLSLGVSKALLD   150
 151  YVIFCHQEESFWPLSEPANLKKRFDEIFESLRYAKALDQIKGLKRDQETQ   200
 201  VKVDQATLTHYRSDKERAEKIELRVHESLKRISCIRSKVEELDQEITETA   250
 251  RLQDELFKSTEEYEQQMITIRHLESQSDIINTTINDLKSQMTITDESSED   300
 301  LEKLHSNFAEKVKEEQELYKSLEKKRSDLESLLKSRRELLEKLTGDLGKI   350
 351  QGEIESLEKLKVKKSTMINEIVHRYNINEINEEGIMTEVSKYASLVNKNY   400
 401  EISSGKLKERQVAVRARIEGIKAHEMFLNNRVSEINSSLEKQLTTQKELR   450
 451  SRFEILFPVKLQREDFTKDVEKSDLWIKSLRQEYESKNLLELLDKHQTAL   500
 501  SSVENRLDEISEIVDSYHKYSGVRTKLQVFEENKTNKSAILANQLMTLKS   550
 551  SFSEVMSYELKDDDNYNEELDKLVEDVRKKLQEKEEAESSLRSVRERLEI   600
 601  RISLSVQSINDLTENKKIKTKTLKSYSGTFASMISEIKALESEIEENRKT   650
 651  LHSLQFGSTFYEKAIEICVDQHACQLCQRSLDKEEEKLFVEHCHSMIDVI   700
 701  PSKSAEVYSHLETLTKTFKNLSEAKPIFDEIELLDKRLSETKTELSDLQG   750
 751  DLQGLDIRKDEIQSELDTLYLRRANLEKLQLLVKDISNLEEEIRTIDRET   800
 801  EVLRIELPSSIAHHNLDEIYAEREKLLEKRGYLRKQIERTKLEETSFKKK   850
 851  IDDAVLANNEQKLKLTKLNFQVNELEQLEKDINKSSEDCDLQKKKLLEVS   900
 901  SKQGSQAPFLNELESEYEKLEADIQEMAQKSRTEILEANEYLHQLNEWNS   950
 951  ELRIDVSTKFKCIKEKKSNIGEEVRIIASKIESTDDNLRKLQERLADLRT  1000
1001  RERNASDNLRLRALMRQLEEAVTQKNYLLSQQSHDDRESFRERMQILKSK  1050
1051  YGALNAERAGLLGECKQLENSITKDKEELNMEFKDADERFRRQLIKTKTT  1100
1101  GKANEDLGKYAKALDVAIMQLHSMKMNEINRIVDELWKQTYCGTDIDTIL  1150
1151  IRSDSEGKGNRTYNYRVCMVKGDAELDMRGRCSAGQKVLACIIIRLALAE  1200
1201  CLGVNCGILALDEPTTNLDEENICSLAKNLSRIVEFRRKQANFQLIVITH  1250
1251  DEQFIRLVNSDAYCSYYYRVKRDTNQKSMIVKEPL                 1285

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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