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

NucPred

Fetching Q9UPT6 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MMEIQMDEGGGVVVYQDDYCSGSVMSERVSGLAGSIYREFERLIHCYDEE    50
  51  VVKELMPLVVNVLENLDSVLSENQEHEVELELLREDNEQLLTQYEREKAL   100
 101  RRQAEEKFIEFEDALEQEKKELQIQVEHYEFQTRQLELKAKNYADQISRL   150
 151  EERESEMKKEYNALHQRHTEMIQTYVEHIERSKMQQVGGNSQTESSLPGR   200
 201  RKERPTSLNVFPLADGTVRAQIGGKLVPAGDHWHLSDLGQLQSSSSYQCP   250
 251  QDEMSESGQSSAAATPSTTGTKSNTPTSSVPSAAVTPLNESLQPLGDYGV   300
 301  GSKNSKRAREKRDSRNMEVQVTQEMRNVSIGMGSSDEWSDVQDIIDSTPE   350
 351  LDMCPETRLDRTGSSPTQGIVNKAFGINTDSLYHELSTAGSEVIGDVDEG   400
 401  ADLLGEFSVRDDFFGMGKEVGNLLLENSQLLETKNALNVVKNDLIAKVDQ   450
 451  LSGEQEVLRGELEAAKQAKVKLENRIKELEEELKRVKSEAIIARREPKEE   500
 501  AEDVSSYLCTESDKIPMAQRRRFTRVEMARVLMERNQYKERLMELQEAVR   550
 551  WTEMIRASREHPSVQEKKKSTIWQFFSRLFSSSSSPPPAKRPYPSVNIHY   600
 601  KSPTTAGFSQRRNHAMCPISAGSRPLEFFPDDDCTSSARREQKREQYRQV   650
 651  REHVRNDDGRLQACGWSLPAKYKQLSPNGGQEDTRMKNVPVPVYCRPLVE   700
 701  KDPTMKLWCAAGVNLSGWRPNEDDAGNGVKPAPGRDPLTCDREGDGEPKS   750
 751  AHTSPEKKKAKELPEMDATSSRVWILTSTLTTSKVVIIDANQPGTVVDQF   800
 801  TVCNAHVLCISSIPAASDSDYPPGEMFLDSDVNPEDPGADGVLAGITLVG   850
 851  CATRCNVPRSNCSSRGDTPVLDKGQGEVATIANGKVNPSQSTEEATEATE   900
 901  VPDPGPSEPETATLRPGPLTEHVFTDPAPTPSSGPQPGSENGPEPDSSST   950
 951  RPEPEPSGDPTGAGSSAAPTMWLGAQNGWLYVHSAVANWKKCLHSIKLKD  1000
1001  SVLSLVHVKGRVLVALADGTLAIFHRGEDGQWDLSNYHLMDLGHPHHSIR  1050
1051  CMAVVYDRVWCGYKNKVHVIQPKTMQIEKSFDAHPRRESQVRQLAWIGDG  1100
1101  VWVSIRLDSTLRLYHAHTHQHLQDVDIEPYVSKMLGTGKLGFSFVRITAL  1150
1151  LVAGSRLWVGTGNGVVISIPLTETVVLHRGQLLGLRANKTSPTSGEGARP  1200
1201  GGIIHVYGDDSSDRAASSFIPYCSMAQAQLCFHGHRDAVKFFVSVPGNVL  1250
1251  ATLNGSVLDSPAEGPGPAAPASEVEGQKLRNVLVLSGGEGYIDFRIGDGE  1300
1301  DDETEEGAGDMSQVKPVLSKAERSHIIVWQVSYTPE                1336

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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