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

NucPred

Fetching Q5KSL6 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MDRGAAAAQGTAPPQDGEQPAESPEPPPPWPPPPPPPAPPPAPPLLSEAS    50
  51  PEPIPEPCPELAPGPCPEATSESATELYTEPTPEPATEPASEPAPEPATE   100
 101  PAPEPATEPAPEPAPEPATESAPEPTPEPALESVPEPAPELTPEVAPELA   150
 151  PEPTPEPVTELAPEFCPEAAPEFRPSPAPCLLQCPVDTRERGLKTSPSPS   200
 201  PSPSPRTPMSWSRIKKILKEGPMLKNCNSFKRWKLRYFLVQGQKLYFAHH   250
 251  PAFAHFETIDLSQATVAESSCRNLCHSFCVITPQRKITLAAPNRKDMEEW   300
 301  INIIKTIQQGEIYKIPAAENNPFLVGMHCWYSSYSHRTQHCNVCRESIPA   350
 351  LSRDAIICEVCKVKSHRLCALRASKDCKWNTLSITDDLLLPADEVNMPHQ   400
 401  WVEGNMPVSSQCAVCHESCGSYQRLQDFRCLWCNSTVHDDCRRRFSKECC   450
 451  FRSHRSSVIPPTALSDPKGDGQLVVSSDFWNLDWSSACSCPLLIFINSKS   500
 501  GDHQGIVFLRKFKQYLNPSQVFDLLKGGPEAGLSMFKNFARFRILVCGGD   550
 551  GSVSWVLSLIDAFGLHEKCQLAVIPLGTGNDLARVLGWGAFWNKSKSPLD   600
 601  ILNRVEQASVRILDRWSVMIRETPRQTPLLKGQVEMDVPRFEAAAIQHLE   650
 651  SAATELNKILKAKYPTEMIIATRFLCSAVEDFVVDIVKAWGQIKQNNTAI   700
 701  VSVILKSDLMYDRLSVLIDVLAEEAAATSAEKSATEYADSSKADRKPFIP   750
 751  QIDHIAKCKLELATKAQSLQKSLKLIIFQVEQALDEESRQTISVKNFSST   800
 801  FFLEDDPEDINQTSPRRRSRRGTLSSISSLKSEDLDNLNLDHLHFTPESI   850
 851  RFKEKCVMNNYFGIGLDAKISLDFNTRRDEHPGQYNSRLKNKMWYGLLGT   900
 901  KELLQRSYRKLEERVHLECDGETISLPNLQGIVVLNITSYAGGINFWGSN   950
 951  TATTEYEAPAIDDGKLEVVAIFGSVQMAMSRIINLHHHRIAQCHEVMITI  1000
1001  DGEEGIPVQVDGEAWIQRPGLIKIRYKNAAQMLTRDRDFENSMKMWEYKH  1050
1051  TEIQAAPQPQLDFQDSQESLSDEEYAQMQHLARLAENLISKLNDLSKIHQ  1100
1101  HVSVLMGSVNASANILNDIFYGQDSGNEMGAASCIPIETLSRNDAVDVTF  1150
1151  SLKGLYDDTTAFLDEKLLRSAEDETALQSALDAMNKEFKKLSEIDWMNPI  1200
1201  FVPEEKSSDTDSRSLRLKIKFPKLGKKKVEEERKPKSGQSVQSFIGNLWH  1250
1251  RRHREDEAEGDDPLTPSRSQL                               1271

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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