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

NucPred

Fetching Q64514 from www.uniprot.org...

The NucPred score for your sequence is 0.18 (see score help below)

   1  MATAATEEPFPFHGLLPKKETGASSFLCRYPEYDGRGVLIAVLDTGVDPG    50
  51  APGMQVTTDGKPKIIDIIDTTGSGDVNTATEVEPKDGEIIGLSGRVLKIP   100
 101  ANWTNPLGKYHIGIKNGYDFYPKALKERIQKERKEKIWDPIHRVALAEAC   150
 151  RKQEEFDIANNGSSQANKLIKEELQSQVELLNSFEKKYSDPGPVYDCLVW   200
 201  HDGETWRACVDSNENGDLSKCAVLRNYKEAQEYSSFGTAEMLNYSVNIYD   250
 251  DGNLLSIVTSGGAHGTHVASIAAGHFPEEPERNGVAPGAQILSIKIGDTR   300
 301  LSTMETGTGLIRAMIEVINHKCDLVNYSYGEATHWPNSGRICEVINEAVW   350
 351  KHNTIYVSSAGNNGPCLSTVGCPGGTTSSVIGVGAYVSPDMMVAEYSLRE   400
 401  KLPANQYTWSSRGPSADGALGVSISAPGGAIASVPNWTLRGTQLMNGTSM   450
 451  SSPNACGGIALVLSGLKANNVDYTVHSVRRALENTAIKADNIEVFAQGHG   500
 501  IIQVDKAYDYLIQNTSFANRLGFTVTVGNNRGIYLRDPVQVAAPSDHGVG   550
 551  IEPVFPENTENSEKISFQLHLALTSNSSWVQCPSHLELMNQCRHINIRVD   600
 601  PRGLREGLHYTEVCGYDIASPNAGPLFRVPITAVIAAKVNESSHYDLAFT   650
 651  DVHFKPGQIRRHFVEVPEGATWAEVTVCSCSSEVSAKFVLHAVQLVKQRA   700
 701  YRSHEFYKFCSLPEKGTLIEAFPVLGGKAIEFCIARWWASLSDVNIDYTI   750
 751  SFHGIVCTAPQLNIHASEGINRFDVQSSLKYEDLAPCITLKSWVQTLRPV   800
 801  NAKTRPLGSRDVLPNNRQLYEMVLTYSFHQPKSGEVTPSCPLLCELLYES   850
 851  EFDSQLWIIFDQNKRQMGSGDAYPHQYSLKLEKGDYTIRLQIRHEQISDL   900
 901  DRLKDLPFIVSHRLSNTLSLDIHENHSLALLGKKKSSSLTLPPKYNQPFF   950
 951  VTSLPDDKIPKGAGPGCYLAGSLTLSKTELGKKAGQSAAKRQGKFKKDVI  1000
1001  PVHYYLIPPPTKIKNGSKDKEKDSEKEKDLKEEFTEALRDLKIQWMTKLD  1050
1051  STDIYNELKETYPAYLPLYVARLHQLDAEKERMKRLNEIVDAANAVISHI  1100
1101  DQTALAVYIAMKTDPRPDAATIKNDMDKQKSTLIDALCRKGCALADHLLH  1150
1151  TQPHDGAAAGDAEAKEEEGESTMESLSETYWETTKWTDLFDTKVLIFAYK  1200
1201  HALVNKMYGRGLKFATKLVEEKPTKENWKNCIQLMKLLGWTHCASFTENW  1250
1251  LPIMYPPDYCVF                                        1262

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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