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

NucPred

Fetching Q5B4Q8 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MRSRYAGATETFADSAYREKEQAFLDANDITKGRYFNEATLPALRSYAVP    50
  51  PVRETKVASLPVPATTPASPNVAPAPALPQAEARASEVASQGALDAETQR   100
 101  VTAPHPVEKHPSYSGPQPSDSRAAPQLAPGTTEISQKADGPAPEVRHAAQ   150
 151  NLQQGQKATSSLPDTPRSSQDPSDATVRADQKDATKAIPSAQPAISTPKP   200
 201  QHDLPASPLPGRPVHVTDQPLSPVSSAGPYSNNTPAPTAASPATSTTEDV   250
 251  SAEKLPTPKRIAATQERSSFVPTTPDEQLRFEEAQSLQQNALLVSQVKDG   300
 301  AGTGPLTNQVISEDLPSTSTTANVAEGASEQVSKDLLPESKMPESTPAAI   350
 351  VESKSQPQSPLGQASSQAETVVKDVAPGTQLTKKTSSSPHPGPPPERMTT   400
 401  RVSSGAIRHKSVSEILGEAPKTPVSPIEKPHTVEKPTDSARAGVYDSTDS   450
 451  AKLRLKDRRAREKERNKFSTVVFPKQQQQPDKDGDMDLVRQQSGALIKLN   500
 501  EERDYLFTLFQNKAYAPPRGTALTALLSSAHKTLTTNNYLLDYQEQMDCR   550
 551  ILRRIYDLQHANRWPLRQLKRSAEPPRQAAHWDVLLDHMKWMRTDFREER   600
 601  KWKLAAAKSCADWCAEYIHSDPESRSMLRVQARIPPKDSPCKNGPQSATM   650
 651  VSPPAELGNDAMEISHPTPDLVPSSEEDSVSEGFPDEPRHGLQDTVAPAA   700
 701  IFSLGSDEFTFSLDMTPTAQKLLDELPIYTPVQIAPDTNLPRFKDLPDAS   750
 751  WKTEILPVSKYARGKIMFREDEPARKRSRYDYSQYSSGSEHPVVELPPEQ   800
 801  TNVALFQPENRHIRDRIHPAQPFRPPTEYPMPSLGFLESRQSSQWTYAED   850
 851  EELRSLVEEYSYNWSLISSCLTPSSQFTSGAERRTPWECFERWAGIEGLP   900
 901  SDMSKTAYFRAYHQRIDTAQRNVMAQQAAAQQQQQQQQQQGSNGNNQQPM   950
 951  PLIRRRGTQPIRVDRRRSSKHLALLDAMRKLAKKRETILQKQQHASQLAS  1000
1001  LRKVNEANQPKPPISSPAEFSRLKHERELKLQERQEQYRQQMIAQQRASL  1050
1051  AARAGQMPNQQQMMNAPGRAPNAIPHNPNAPPVSTSTANGLPNGISNPLA  1100
1101  NGMPNGLPQNVGVNQGRPHVQGMHGSGGPVNNHISPNPMAMKMMPQASMQ  1150
1151  QNNAPRPNMAMQASPDNARVIREANRLQEQQRILQSRQQPSQHPLQQQQP  1200
1201  PQAQNQQQQLPQQPQQAQQQFHAQPQFVPQGSNSPNLNMPTVNGTPNNPA  1250
1251  MIAALQAGGGMQSPPFHNSAPQGVSTPSPRMGQPNTLSSGAVPTTISTIQ  1300
1301  SQIQRSNPNMPLEQVKQLTTERLHQYQQQQQQRMSQVAMNAAAGNLGVQP  1350
1351  NYQVSHDGNFQPQSGMSGGPNMQVPQAQGFSPMMRVPQPSQQNRIGAGGS  1400
1401  PAMGVAVPQQSRSATPQTQRSGSIQTGTIAGASKSPNTHSQTQSMGA     1447

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.)

Go back to the NucPred Home Page.